log started: Mon Jul 28 15:06:36 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > source buildit ----- Source: ./buildit ----- Source of ./buildit done >> >> #CM5 = loadmol2 cm5.mol2 >> #TMI = loadmol2 tmi.mol2 >> loadoff heme.off Loading library: ./heme.off Loading: HEM >> gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) >> heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) >> ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) >> loadoff CYP.off Loading library: ./CYP.off Loading: CYP >> >> >> aa = loadpdb m5.pdb Loading PDB file: ./m5.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element >> bond aa.410.SG aa.465.FE >> >> saveamberparm aa m5_invacuo.topo m5_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) >> >> quit Quit log started: Mon Jul 28 15:07:00 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m5.pdb Loading PDB file: ./m5.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m5_invacuo.topo m5_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.397110 to meet diagonal cut criterion Solute vdw bounding box: 48.637 69.914 71.195 Total bounding box for atom centers: 104.725 104.725 104.725 (box expansion for 'iso' is 29.0%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 590891.441 A^3 (oct) Total mass 320266.290 amu, Density 0.900 g/cc Added 14855 residues. > > addions aa Cl- 0 addIons: 1st Ion & target are the same charge: can't neutralize. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -34.08 -42.23 -39.36 41.69 39.47 37.00 sized: 93.92 85.77 88.64 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.15% of box, grid points 87134 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 111 sec (Replacing solvent molecule) Placed Na+ in aa at (-7.43, 14.17, 21.20). (Replacing solvent molecule) Placed Cl- in aa at (11.44, 2.52, 19.38). (Replacing solvent molecule) Placed Na+ in aa at (-3.16, -39.20, -6.98). (Replacing solvent molecule) Placed Cl- in aa at (34.56, 14.17, -7.75). (Replacing solvent molecule) Placed Na+ in aa at (-26.32, -12.13, -4.77). (Replacing solvent molecule) Placed Cl- in aa at (17.31, 20.22, 13.92). (Replacing solvent molecule) Placed Na+ in aa at (19.44, -20.57, -6.46). (Replacing solvent molecule) Placed Cl- in aa at (-7.83, -31.37, -22.12). (Replacing solvent molecule) Placed Na+ in aa at (-10.46, -31.08, -21.61). (Replacing solvent molecule) Placed Cl- in aa at (-8.98, -33.23, -17.53). (Replacing solvent molecule) Placed Na+ in aa at (-11.88, -34.56, -14.92). (Replacing solvent molecule) Placed Cl- in aa at (-3.95, -38.32, -9.88). (Replacing solvent molecule) Placed Na+ in aa at (-5.14, -31.91, -11.32). (Replacing solvent molecule) Placed Cl- in aa at (10.22, -17.11, 7.89). (Replacing solvent molecule) Placed Na+ in aa at (18.81, -23.83, 5.03). (Replacing solvent molecule) Placed Cl- in aa at (20.18, -21.48, 2.97). (Replacing solvent molecule) Placed Na+ in aa at (22.17, -21.59, -2.52). (Replacing solvent molecule) Placed Cl- in aa at (23.77, -20.76, -6.70). (Replacing solvent molecule) Placed Na+ in aa at (25.74, -14.52, -4.30). (Replacing solvent molecule) Placed Cl- in aa at (25.84, -23.31, -1.45). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -46.99 -39.83 42.35 39.94 37.47 sized: 93.45 81.01 88.17 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.75% of box, grid points 99510 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 101 sec (No solvent overlap) Placed Na+ in aa at (-14.55, 9.01, -10.83). (Replacing solvent molecule) Placed Cl- in aa at (-13.25, 1.48, -13.23). (Replacing solvent molecule) Placed Na+ in aa at (-10.09, 2.38, -13.02). (Replacing solvent molecule) Placed Cl- in aa at (-6.04, 3.16, -14.96). (Replacing solvent molecule) Placed Na+ in aa at (-3.93, 9.17, -17.21). (Replacing solvent molecule) Placed Cl- in aa at (-4.95, 15.13, -16.71). (Replacing solvent molecule) Placed Na+ in aa at (-2.41, 16.81, -13.23). (Replacing solvent molecule) Placed Cl- in aa at (-0.43, 8.61, -18.40). (Replacing solvent molecule) Placed Na+ in aa at (2.66, 8.24, -20.61). (Replacing solvent molecule) Placed Cl- in aa at (1.81, 12.58, -19.41). (Replacing solvent molecule) Placed Na+ in aa at (-14.84, 6.27, -14.77). (Replacing solvent molecule) Placed Cl- in aa at (-19.15, 10.67, -12.11). (No solvent overlap) Placed Na+ in aa at (-18.55, 14.01, -9.83). (Replacing solvent molecule) Placed Cl- in aa at (-16.89, 9.89, -13.93). (Replacing solvent molecule) Placed Na+ in aa at (-15.97, 14.01, -14.36). (Replacing solvent molecule) Placed Cl- in aa at (-16.39, 17.88, -10.72). (Replacing solvent molecule) Placed Na+ in aa at (-20.10, 20.45, -12.82). (Replacing solvent molecule) Placed Cl- in aa at (-21.30, 22.57, -8.33). (Replacing solvent molecule) Placed Na+ in aa at (-21.70, 19.30, -9.09). (Replacing solvent molecule) Placed Cl- in aa at (-22.08, 15.14, -13.30). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -46.99 -39.83 42.35 39.94 37.47 sized: 93.45 81.01 88.17 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.82% of box, grid points 101123 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 132 sec (No solvent overlap) Placed Na+ in aa at (13.45, 0.01, -24.83). (Replacing solvent molecule) Placed Cl- in aa at (-12.19, 5.93, -16.62). (Replacing solvent molecule) Placed Na+ in aa at (-23.47, -0.37, 26.45). (Replacing solvent molecule) Placed Cl- in aa at (-19.48, 15.74, -6.76). (Replacing solvent molecule) Placed Na+ in aa at (-23.79, 11.99, 2.33). (Replacing solvent molecule) Placed Cl- in aa at (10.23, -4.59, -26.31). (Replacing solvent molecule) Placed Na+ in aa at (9.95, -2.54, -29.65). (Replacing solvent molecule) Placed Cl- in aa at (5.51, 1.61, -25.52). (Replacing solvent molecule) Placed Na+ in aa at (7.42, 1.55, -27.64). (Replacing solvent molecule) Placed Cl- in aa at (6.91, 1.50, -30.48). (Replacing solvent molecule) Placed Na+ in aa at (6.32, 4.93, -27.27). (Replacing solvent molecule) Placed Cl- in aa at (5.89, 7.46, -29.99). (Replacing solvent molecule) Placed Na+ in aa at (-20.54, 14.73, -1.89). (Replacing solvent molecule) Placed Cl- in aa at (-25.68, 13.94, -1.50). (Replacing solvent molecule) Placed Na+ in aa at (7.61, 5.48, -34.37). (Replacing solvent molecule) Placed Cl- in aa at (-18.19, 15.85, -1.09). (Replacing solvent molecule) Placed Na+ in aa at (-17.04, 18.06, 4.64). (Replacing solvent molecule) Placed Cl- in aa at (-13.71, 22.16, 5.03). (Replacing solvent molecule) Placed Na+ in aa at (-15.98, 21.74, 1.96). (Replacing solvent molecule) Placed Cl- in aa at (-20.54, 18.73, 2.09). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -46.99 -42.16 42.35 39.94 37.47 sized: 93.45 81.01 85.84 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.91% of box, grid points 103014 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 128 sec (Replacing solvent molecule) Placed Na+ in aa at (-17.04, 7.27, -12.93). (Replacing solvent molecule) Placed Cl- in aa at (-2.11, 19.66, -10.95). (Replacing solvent molecule) Placed Na+ in aa at (2.38, 17.96, -17.27). (Replacing solvent molecule) Placed Cl- in aa at (-0.08, 13.95, -15.90). (Replacing solvent molecule) Placed Na+ in aa at (0.02, 20.71, -13.13). (Replacing solvent molecule) Placed Cl- in aa at (5.64, 20.99, -14.21). (Replacing solvent molecule) Placed Na+ in aa at (9.05, 22.62, -13.37). (Replacing solvent molecule) Placed Cl- in aa at (14.91, 21.73, -14.41). (Replacing solvent molecule) Placed Na+ in aa at (14.25, 21.83, -18.63). (Replacing solvent molecule) Placed Cl- in aa at (-1.35, 21.26, -16.62). (Replacing solvent molecule) Placed Na+ in aa at (25.17, 8.19, 12.18). (Replacing solvent molecule) Placed Cl- in aa at (12.85, -2.65, -29.93). (Replacing solvent molecule) Placed Na+ in aa at (10.41, 0.94, -31.68). (Replacing solvent molecule) Placed Cl- in aa at (11.44, 2.52, -33.72). (Replacing solvent molecule) Placed Na+ in aa at (-3.23, 13.14, -21.10). (Replacing solvent molecule) Placed Cl- in aa at (12.10, 18.89, -21.66). (Replacing solvent molecule) Placed Na+ in aa at (10.07, 21.52, -25.70). (Replacing solvent molecule) Placed Cl- in aa at (9.59, 25.22, -31.59). (Replacing solvent molecule) Placed Na+ in aa at (10.67, 25.17, -34.23). (Replacing solvent molecule) Placed Cl- in aa at (11.67, 21.07, -27.91). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -46.99 -42.16 42.35 39.94 37.47 sized: 93.45 81.01 85.84 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.00% of box, grid points 104878 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 165 sec (Replacing solvent molecule) Placed Na+ in aa at (22.61, -13.80, -15.68). (Replacing solvent molecule) Placed Cl- in aa at (26.46, -21.99, -20.46). (Replacing solvent molecule) Placed Na+ in aa at (24.70, -23.12, -10.64). (Replacing solvent molecule) Placed Cl- in aa at (22.06, -15.69, -20.84). (Replacing solvent molecule) Placed Na+ in aa at (20.40, -22.91, -18.10). (Replacing solvent molecule) Placed Cl- in aa at (20.83, -23.24, -14.87). (Replacing solvent molecule) Placed Na+ in aa at (23.96, -18.24, -19.32). (Replacing solvent molecule) Placed Cl- in aa at (24.18, -22.06, -17.12). (Replacing solvent molecule) Placed Na+ in aa at (17.31, -25.77, -12.63). (Replacing solvent molecule) Placed Cl- in aa at (15.19, -21.98, -25.04). (Replacing solvent molecule) Placed Na+ in aa at (18.81, -23.83, -21.52). (Replacing solvent molecule) Placed Cl- in aa at (18.09, -24.37, -17.50). (Replacing solvent molecule) Placed Na+ in aa at (14.01, -18.66, -23.87). (Replacing solvent molecule) Placed Cl- in aa at (11.38, -18.67, -23.03). (Replacing solvent molecule) Placed Na+ in aa at (10.06, -13.77, -22.03). (Replacing solvent molecule) Placed Cl- in aa at (14.89, -9.23, -23.90). (Replacing solvent molecule) Placed Na+ in aa at (14.23, -12.28, -22.85). (Replacing solvent molecule) Placed Cl- in aa at (13.86, -15.45, -23.91). (Replacing solvent molecule) Placed Na+ in aa at (17.76, -16.25, -24.18). (Replacing solvent molecule) Placed Cl- in aa at (21.48, -18.23, -22.17). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -46.99 -42.16 42.35 39.94 37.47 sized: 93.45 81.01 85.84 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.07% of box, grid points 106391 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 141 sec (Replacing solvent molecule) Placed Na+ in aa at (-1.55, -27.46, 9.27). (Replacing solvent molecule) Placed Cl- in aa at (-6.29, 10.93, -19.81). (Replacing solvent molecule) Placed Na+ in aa at (-9.26, 12.79, -26.09). (Replacing solvent molecule) Placed Cl- in aa at (-4.37, 12.55, -25.90). (Replacing solvent molecule) Placed Na+ in aa at (-3.18, 9.50, -25.12). (Replacing solvent molecule) Placed Cl- in aa at (0.07, 6.66, -22.92). (Replacing solvent molecule) Placed Na+ in aa at (-2.84, 4.51, -23.30). (Replacing solvent molecule) Placed Cl- in aa at (-6.79, 6.10, -23.90). (Replacing solvent molecule) Placed Na+ in aa at (-8.65, 8.07, -20.04). (Replacing solvent molecule) Placed Cl- in aa at (-3.59, 2.06, -22.12). (Replacing solvent molecule) Placed Na+ in aa at (-7.45, 3.05, -22.85). (Replacing solvent molecule) Placed Cl- in aa at (-9.33, 10.25, -24.31). (Replacing solvent molecule) Placed Na+ in aa at (-7.83, 14.62, -22.12). (Replacing solvent molecule) Placed Cl- in aa at (-9.47, 17.59, -25.78). (Replacing solvent molecule) Placed Na+ in aa at (-3.18, -36.48, 1.43). (Replacing solvent molecule) Placed Cl- in aa at (-6.79, -39.89, 2.65). (Replacing solvent molecule) Placed Na+ in aa at (-7.41, -36.21, 0.51). (Replacing solvent molecule) Placed Cl- in aa at (-3.21, -36.76, -1.30). (Replacing solvent molecule) Placed Na+ in aa at (-11.23, -37.21, 4.68). (Replacing solvent molecule) Placed Cl- in aa at (-13.38, -35.24, 3.34). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -47.68 -42.16 42.35 39.94 37.47 sized: 93.45 80.32 85.84 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.17% of box, grid points 108335 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 174 sec (No solvent overlap) Placed Na+ in aa at (-2.55, -35.68, -5.16). (Replacing solvent molecule) Placed Cl- in aa at (0.75, -28.28, 13.53). (Replacing solvent molecule) Placed Na+ in aa at (-2.36, -32.29, 15.74). (Replacing solvent molecule) Placed Cl- in aa at (-9.71, -34.92, -11.19). (Replacing solvent molecule) Placed Na+ in aa at (-9.58, -34.77, -8.39). (Replacing solvent molecule) Placed Cl- in aa at (-8.00, -37.33, -4.22). (Replacing solvent molecule) Placed Na+ in aa at (-7.24, -39.89, -7.95). (Replacing solvent molecule) Placed Cl- in aa at (-4.92, -41.82, -6.98). (Replacing solvent molecule) Placed Na+ in aa at (-7.60, -39.92, -3.68). (Replacing solvent molecule) Placed Cl- in aa at (-11.51, -41.15, -6.19). (Replacing solvent molecule) Placed Na+ in aa at (-14.54, -37.97, -5.28). (Replacing solvent molecule) Placed Cl- in aa at (-14.43, -36.26, -8.84). (Replacing solvent molecule) Placed Na+ in aa at (-14.84, -39.71, -14.77). (Replacing solvent molecule) Placed Cl- in aa at (-11.42, -37.00, -16.16). (Replacing solvent molecule) Placed Na+ in aa at (-7.35, -37.80, -14.37). (Replacing solvent molecule) Placed Cl- in aa at (-16.88, -35.16, -1.68). (Replacing solvent molecule) Placed Na+ in aa at (-14.98, -33.33, -5.74). (Replacing solvent molecule) Placed Cl- in aa at (-4.52, -33.39, 12.56). (Replacing solvent molecule) Placed Na+ in aa at (-8.52, -35.81, 9.99). (Replacing solvent molecule) Placed Cl- in aa at (-9.12, -34.38, 6.25). Done adding ions. > > saveamberparm aa m5.topo m5.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14719 ) (no restraints) > > quit Quit log started: Mon Jul 28 16:22:49 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m4.pdb Loading PDB file: ./m4.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m4_invacuo.topo m4_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.419079 to meet diagonal cut criterion Solute vdw bounding box: 47.880 66.283 69.913 Total bounding box for atom centers: 103.971 103.971 103.971 (box expansion for 'iso' is 31.5%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 578325.028 A^3 (oct) Total mass 315311.890 amu, Density 0.905 g/cc Added 14580 residues. > > addions aa Cl- 0 addIons: 1st Ion & target are the same charge: can't neutralize. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.92 -42.12 -38.26 43.51 39.59 37.38 sized: 95.08 85.88 89.74 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.04% of box, grid points 84805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Mon Jul 28 16:23:08 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m3.pdb Loading PDB file: ./m3.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m3_invacuo.topo m3_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.450544 to meet diagonal cut criterion Solute vdw bounding box: 52.146 67.004 71.089 Total bounding box for atom centers: 105.902 105.902 105.902 (box expansion for 'iso' is 26.7%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 610837.974 A^3 (oct) Total mass 330643.506 amu, Density 0.899 g/cc Added 15431 residues. > > addions aa Cl- 0 addIons: 1st Ion & target are the same charge: can't neutralize. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.22 -43.51 -43.67 43.83 38.27 37.09 sized: 95.78 84.49 84.33 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.23% of box, grid points 88701 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Mon Jul 28 16:23:33 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m2.pdb Loading PDB file: ./m2.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m2_invacuo.topo m2_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.379597 to meet diagonal cut criterion Solute vdw bounding box: 50.614 66.247 72.160 Total bounding box for atom centers: 105.271 105.271 105.271 (box expansion for 'iso' is 33.2%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 600078.753 A^3 (oct) Total mass 326319.666 amu, Density 0.903 g/cc Added 15191 residues. > > addions aa Cl- 0 addIons: 1st Ion & target are the same charge: can't neutralize. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -33.22 -41.31 -38.45 41.97 38.17 37.55 sized: 94.78 86.69 89.55 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.08% of box, grid points 85635 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Mon Jul 28 16:23:58 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m1.pdb Loading PDB file: ./m1.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m1_invacuo.topo m1_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.363324 to meet diagonal cut criterion Solute vdw bounding box: 49.450 66.410 71.273 Total bounding box for atom centers: 103.993 103.993 103.993 (box expansion for 'iso' is 32.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 578693.992 A^3 (oct) Total mass 315257.842 amu, Density 0.905 g/cc Added 14577 residues. > > addions aa Cl- 0 addIons: 1st Ion & target are the same charge: can't neutralize. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -33.34 -40.88 -37.95 41.42 39.54 37.63 sized: 94.66 87.12 90.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.10% of box, grid points 86062 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 131 sec (Replacing solvent molecule) Placed Na+ in aa at (-5.35, -36.65, -2.92). (Replacing solvent molecule) Placed Cl- in aa at (12.60, 1.91, 16.03). (Replacing solvent molecule) Placed Na+ in aa at (-25.91, -9.91, -7.31). (Replacing solvent molecule) Placed Cl- in aa at (34.90, 11.50, -6.98). (Replacing solvent molecule) Placed Na+ in aa at (19.38, -20.58, -6.20). (Replacing solvent molecule) Placed Cl- in aa at (31.46, 14.38, -22.94). (Replacing solvent molecule) Placed Na+ in aa at (33.06, 10.18, -20.18). (Replacing solvent molecule) Placed Cl- in aa at (34.28, 9.57, -23.80). (Replacing solvent molecule) Placed Na+ in aa at (31.32, 10.98, -28.53). (Replacing solvent molecule) Placed Cl- in aa at (29.25, 9.22, -27.59). (Replacing solvent molecule) Placed Na+ in aa at (31.69, 6.19, -25.44). (Replacing solvent molecule) Placed Cl- in aa at (30.45, 0.93, -24.51). (Replacing solvent molecule) Placed Na+ in aa at (31.18, 15.40, -31.12). (Replacing solvent molecule) Placed Cl- in aa at (25.03, 14.16, -31.64). (Replacing solvent molecule) Placed Na+ in aa at (27.32, 6.34, -27.38). (Replacing solvent molecule) Placed Cl- in aa at (24.94, 6.95, -26.07). (Replacing solvent molecule) Placed Na+ in aa at (25.83, 11.36, -27.86). (Replacing solvent molecule) Placed Cl- in aa at (33.72, 13.82, -29.48). (Replacing solvent molecule) Placed Na+ in aa at (35.47, 15.20, -23.65). (Replacing solvent molecule) Placed Cl- in aa at (34.27, 12.57, -19.15). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.70 -44.44 -39.43 43.98 40.06 37.85 sized: 94.30 83.56 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.59% of box, grid points 96278 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 136 sec (No solvent overlap) Placed Na+ in aa at (-4.22, -36.51, -1.67). (Replacing solvent molecule) Placed Cl- in aa at (13.41, 0.45, 19.31). (Replacing solvent molecule) Placed Na+ in aa at (20.97, -24.91, -5.29). (Replacing solvent molecule) Placed Cl- in aa at (34.96, 11.06, -3.91). (Replacing solvent molecule) Placed Na+ in aa at (-23.05, -15.38, -4.74). (Replacing solvent molecule) Placed Cl- in aa at (-5.22, -39.78, -0.99). (Replacing solvent molecule) Placed Na+ in aa at (-14.51, -36.39, -8.75). (Replacing solvent molecule) Placed Cl- in aa at (23.40, -25.88, -6.04). (Replacing solvent molecule) Placed Na+ in aa at (20.15, -29.38, -9.47). (Replacing solvent molecule) Placed Cl- in aa at (18.38, 16.76, 12.07). (Replacing solvent molecule) Placed Na+ in aa at (-11.32, -38.65, 0.07). (Replacing solvent molecule) Placed Cl- in aa at (-15.88, -30.20, -6.98). (Replacing solvent molecule) Placed Na+ in aa at (-17.72, -32.36, -10.53). (Replacing solvent molecule) Placed Cl- in aa at (-16.98, -36.23, -13.84). (Replacing solvent molecule) Placed Na+ in aa at (-15.07, -33.46, -5.65). (Replacing solvent molecule) Placed Cl- in aa at (-14.63, -38.10, -5.19). (Replacing solvent molecule) Placed Na+ in aa at (-20.67, 1.63, 23.77). (Replacing solvent molecule) Placed Cl- in aa at (-25.70, 1.37, 22.71). (Replacing solvent molecule) Placed Na+ in aa at (-23.66, 3.04, 21.94). (Replacing solvent molecule) Placed Cl- in aa at (-11.32, -37.34, 4.77). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -47.57 -44.14 44.30 38.74 37.56 sized: 94.51 80.43 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.81% of box, grid points 100940 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 137 sec (Replacing solvent molecule) Placed Na+ in aa at (30.10, 0.21, 5.87). (Replacing solvent molecule) Placed Cl- in aa at (-18.78, 22.47, -8.72). (Replacing solvent molecule) Placed Na+ in aa at (0.27, -38.56, -8.21). (Replacing solvent molecule) Placed Cl- in aa at (31.86, 16.78, -7.41). (Replacing solvent molecule) Placed Na+ in aa at (28.48, 9.35, 9.47). (Replacing solvent molecule) Placed Cl- in aa at (14.14, 22.02, 8.04). (Replacing solvent molecule) Placed Na+ in aa at (27.45, -14.55, -6.95). (Replacing solvent molecule) Placed Cl- in aa at (9.73, -16.09, -23.08). (Replacing solvent molecule) Placed Na+ in aa at (-29.10, -5.70, 0.26). (Replacing solvent molecule) Placed Cl- in aa at (12.55, 2.10, 15.89). (Replacing solvent molecule) Placed Na+ in aa at (10.79, -0.82, 17.03). (Replacing solvent molecule) Placed Cl- in aa at (10.29, 1.13, 21.55). (Replacing solvent molecule) Placed Na+ in aa at (9.84, -2.36, 23.58). (Replacing solvent molecule) Placed Cl- in aa at (9.56, -3.14, 19.05). (Replacing solvent molecule) Placed Na+ in aa at (14.18, -3.53, 12.30). (Replacing solvent molecule) Placed Cl- in aa at (14.78, -6.67, 9.10). (Replacing solvent molecule) Placed Na+ in aa at (17.64, -5.98, 9.47). (Replacing solvent molecule) Placed Cl- in aa at (18.15, -5.94, 12.31). (Replacing solvent molecule) Placed Na+ in aa at (16.61, -6.89, 6.32). (Replacing solvent molecule) Placed Cl- in aa at (20.16, -9.12, 7.82). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -46.35 -38.92 42.44 38.64 38.02 sized: 91.11 81.65 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.64% of box, grid points 97297 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 173 sec (No solvent overlap) Placed Na+ in aa at (-1.70, 15.56, 20.57). (Replacing solvent molecule) Placed Cl- in aa at (17.86, 14.53, 14.75). (Replacing solvent molecule) Placed Na+ in aa at (20.18, 16.73, 17.25). (Replacing solvent molecule) Placed Cl- in aa at (21.58, 19.04, 14.25). (Replacing solvent molecule) Placed Na+ in aa at (20.48, 18.65, 11.30). (Replacing solvent molecule) Placed Cl- in aa at (22.88, 21.48, 10.35). (Replacing solvent molecule) Placed Na+ in aa at (-20.65, 1.75, 23.93). (Replacing solvent molecule) Placed Cl- in aa at (-23.15, -1.64, 21.24). (Replacing solvent molecule) Placed Na+ in aa at (-25.67, 1.49, 22.88). (Replacing solvent molecule) Placed Cl- in aa at (-24.48, 2.68, 19.38). (Replacing solvent molecule) Placed Na+ in aa at (-23.18, 1.40, 17.25). (Replacing solvent molecule) Placed Cl- in aa at (-23.10, 3.25, 26.77). (Replacing solvent molecule) Placed Na+ in aa at (-21.82, 6.28, 24.19). (Replacing solvent molecule) Placed Cl- in aa at (-6.25, 20.98, 21.53). (Replacing solvent molecule) Placed Na+ in aa at (-2.75, 18.44, 19.78). (Replacing solvent molecule) Placed Cl- in aa at (-2.37, 23.02, 19.28). (Replacing solvent molecule) Placed Na+ in aa at (-10.41, 24.39, 24.29). (Replacing solvent molecule) Placed Cl- in aa at (-11.66, 18.93, 29.84). (Replacing solvent molecule) Placed Na+ in aa at (-8.86, 21.82, 32.34). (Replacing solvent molecule) Placed Cl- in aa at (-8.65, 21.69, 27.20). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.70 -44.44 -39.43 43.98 40.06 40.13 sized: 94.30 83.56 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 charges: 243 sec (Replacing solvent molecule) Placed Na+ in aa at (25.05, -13.22, -12.51). (Replacing solvent molecule) Placed Cl- in aa at (12.59, 4.91, 20.68). (Replacing solvent molecule) Placed Na+ in aa at (-0.10, -38.26, -3.84). grid build: 2 sec (Replacing solvent molecule) Volume = 4.75% of box, grid points 99655 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges Placed Cl- in aa at (34.96, 16.26, -3.58). (Replacing solvent molecule) Placed Na+ in aa at (39.30, 13.93, -1.24). (Replacing solvent molecule) Placed Cl- in aa at (38.04, 10.46, -2.87). (Replacing solvent molecule) Placed Na+ in aa at (38.74, 13.93, -4.16). (Replacing solvent molecule) Placed Cl- in aa at (19.31, -15.30, -20.55). (Replacing solvent molecule) Placed Na+ in aa at (25.11, 8.18, 12.44). (Replacing solvent molecule) Placed Cl- in aa at (39.37, 14.40, 2.64). (Replacing solvent molecule) Placed Na+ in aa at (6.78, -32.06, -1.24). (Replacing solvent molecule) Placed Cl- in aa at (-12.82, 25.97, -12.44). (Replacing solvent molecule) Placed Na+ in aa at (-11.30, 30.46, -13.04). (Replacing solvent molecule) Placed Cl- in aa at (-11.51, 33.72, -12.78). (Replacing solvent molecule) Placed Na+ in aa at (-10.57, 27.43, -10.32). (Replacing solvent molecule) Placed Cl- in aa at (-10.74, 29.21, -5.66). (Replacing solvent molecule) Placed Na+ in aa at (33.72, 3.55, 5.15). (Replacing solvent molecule) Placed Cl- in aa at (-8.94, 26.90, -15.09). (Replacing solvent molecule) Placed Na+ in aa at (-5.66, 23.74, -16.06). (Replacing solvent molecule) Placed Cl- in aa at (-4.06, 21.60, -14.51). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.81 -46.05 -38.42 47.16 41.51 38.10 sized: 94.19 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 4.72% of box, grid points 98942 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 200 sec (No solvent overlap) Placed Na+ in aa at (21.11, -4.35, -16.92). (Replacing solvent molecule) Placed Cl- in aa at (12.54, -17.89, 7.27). (Replacing solvent molecule) Placed Na+ in aa at (15.38, -17.16, 8.12). (Replacing solvent molecule) Placed Cl- in aa at (-13.67, 22.53, -1.55). (Replacing solvent molecule) Placed Na+ in aa at (-11.47, 21.17, 6.58). (Replacing solvent molecule) Placed Cl- in aa at (-13.31, 21.54, 2.58). (Replacing solvent molecule) Placed Na+ in aa at (-9.91, 23.32, 3.50). (Replacing solvent molecule) Placed Cl- in aa at (-11.12, 17.68, 5.72). (Replacing solvent molecule) Placed Na+ in aa at (23.41, -23.03, -7.86). (Replacing solvent molecule) Placed Cl- in aa at (22.11, -26.15, -9.63). (Replacing solvent molecule) Placed Na+ in aa at (24.11, -25.19, -13.98). (Replacing solvent molecule) Placed Cl- in aa at (24.10, -26.94, -17.16). (Replacing solvent molecule) Placed Na+ in aa at (-16.10, 21.92, 2.08). (Replacing solvent molecule) Placed Cl- in aa at (-8.85, 25.10, 7.09). (Replacing solvent molecule) Placed Na+ in aa at (-8.30, 32.04, 2.16). (Replacing solvent molecule) Placed Cl- in aa at (-10.63, 30.19, 2.83). (Replacing solvent molecule) Placed Na+ in aa at (-8.67, 27.93, 7.36). (Replacing solvent molecule) Placed Cl- in aa at (20.72, -23.06, -14.75). (Replacing solvent molecule) Placed Na+ in aa at (23.61, -23.98, -20.90). (Replacing solvent molecule) Placed Cl- in aa at (20.07, -21.29, -23.46). charges: 232 sec Done adding ions. > addions aa Na+ 10 Cl- 10 (No solvent overlap) Adding 20 counter ions to "aa" using 1A grid Placed Na+ in aa at (-2.49, 14.43, 20.86). Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -46.35 -38.92 42.44 39.83 38.02 sized: 91.11 81.65 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 (Replacing solvent molecule) Placed Cl- in aa at (-5.40, 16.31, 19.40). (Replacing solvent molecule) Placed Na+ in aa at (-5.93, 15.24, 23.02). (Replacing solvent molecule) Placed Cl- in aa at (-9.83, 16.96, 23.77). (Replacing solvent molecule) Placed Na+ in aa at (-6.27, 20.85, 21.37). (Replacing solvent molecule) Placed Cl- in aa at (-4.25, 20.62, 19.08). grid build: 2 sec (Replacing solvent molecule) Volume = 4.75% of box, grid points 99574 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges Placed Na+ in aa at (-4.01, 21.94, 15.74). (Replacing solvent molecule) Placed Cl- in aa at (-2.09, 23.80, 15.15). (Replacing solvent molecule) Placed Na+ in aa at (-8.27, 15.77, 19.31). (Replacing solvent molecule) Placed Cl- in aa at (-12.37, 16.60, 17.08). (Replacing solvent molecule) Placed Na+ in aa at (-11.92, 21.91, 16.72). (Replacing solvent molecule) Placed Cl- in aa at (-11.78, 22.61, 11.77). (Replacing solvent molecule) Placed Na+ in aa at (-11.45, 20.86, 6.55). (Replacing solvent molecule) Placed Cl- in aa at (-6.09, 19.27, 7.82). (Replacing solvent molecule) Placed Na+ in aa at (-12.07, 18.52, 11.13). (Replacing solvent molecule) Placed Cl- in aa at (-16.21, 16.87, 10.19). (Replacing solvent molecule) Placed Na+ in aa at (-23.68, 10.51, 13.94). (Replacing solvent molecule) Placed Cl- in aa at (-22.16, 15.00, 13.34). (Replacing solvent molecule) Placed Na+ in aa at (-20.83, 16.72, 10.96). (Replacing solvent molecule) Placed Cl- in aa at (-14.01, 19.90, 6.95). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -47.57 -44.14 44.30 38.74 37.56 sized: 94.51 80.43 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.89% of box, grid points 102515 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 149 sec (No solvent overlap) Placed Na+ in aa at (-21.70, 9.56, 7.57). (Replacing solvent molecule) Placed Cl- in aa at (-23.74, 16.26, 2.04). (Replacing solvent molecule) Placed Na+ in aa at (-21.36, 14.96, 5.97). (Replacing solvent molecule) Placed Cl- in aa at (-25.91, 13.09, 5.97). (Replacing solvent molecule) Placed Na+ in aa at (-20.61, 18.72, 2.35). (Replacing solvent molecule) Placed Cl- in aa at (-17.86, 19.66, 2.15). (Replacing solvent molecule) Placed Na+ in aa at (-23.85, 11.99, 2.59). (Replacing solvent molecule) Placed Cl- in aa at (-24.15, 9.14, 0.30). (Replacing solvent molecule) Placed Na+ in aa at (-27.96, 5.18, 5.89). (Replacing solvent molecule) Placed Cl- in aa at (-27.94, 2.73, 4.90). (Replacing solvent molecule) Placed Na+ in aa at (6.78, -32.06, -1.24). (Replacing solvent molecule) Placed Cl- in aa at (9.23, -35.13, -3.74). (Replacing solvent molecule) Placed Na+ in aa at (5.83, -38.53, -3.18). (Replacing solvent molecule) Placed Cl- in aa at (1.80, -40.90, -3.99). (Replacing solvent molecule) Placed Na+ in aa at (-1.65, -38.86, -1.64). (Replacing solvent molecule) Placed Cl- in aa at (-3.48, -40.37, -3.35). (Replacing solvent molecule) Placed Na+ in aa at (0.32, -38.75, -8.07). (Replacing solvent molecule) Placed Cl- in aa at (1.31, -36.07, -12.24). (Replacing solvent molecule) Placed Na+ in aa at (-1.49, -37.62, -10.23). (Replacing solvent molecule) Placed Cl- in aa at (-6.26, -35.60, -8.37). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.75 -48.69 -39.43 43.98 40.06 40.13 sized: 92.25 79.31 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.88% of box, grid points 102327 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 118 sec (No solvent overlap) Placed Na+ in aa at (16.11, -25.35, -7.92). (Replacing solvent molecule) Placed Cl- in aa at (-8.26, 32.30, 6.35). (Replacing solvent molecule) Placed Na+ in aa at (18.36, -28.91, -14.45). (Replacing solvent molecule) Placed Cl- in aa at (14.78, -32.04, -10.50). (Replacing solvent molecule) Placed Na+ in aa at (17.98, -36.08, -8.72). (Replacing solvent molecule) Placed Cl- in aa at (18.15, -32.52, -16.76). (Replacing solvent molecule) Placed Na+ in aa at (14.12, -35.10, -9.45). (Replacing solvent molecule) Placed Cl- in aa at (14.16, -28.36, -12.64). (Replacing solvent molecule) Placed Na+ in aa at (13.57, -29.48, -17.38). (Replacing solvent molecule) Placed Cl- in aa at (16.18, -35.91, -6.50). (Replacing solvent molecule) Placed Na+ in aa at (14.32, -33.48, -6.33). (Replacing solvent molecule) Placed Cl- in aa at (17.98, -31.00, -8.90). (Replacing solvent molecule) Placed Na+ in aa at (17.53, -36.72, -2.42). (Replacing solvent molecule) Placed Cl- in aa at (20.07, -35.59, -2.86). (No solvent overlap) Placed Na+ in aa at (19.11, -32.35, -4.92). (Replacing solvent molecule) Placed Cl- in aa at (22.83, -34.58, -8.26). (Replacing solvent molecule) Placed Na+ in aa at (21.17, -38.34, 0.10). (Replacing solvent molecule) Placed Cl- in aa at (17.83, -39.20, 2.82). (Replacing solvent molecule) Placed Na+ in aa at (24.88, -30.76, -15.44). (Replacing solvent molecule) Placed Cl- in aa at (31.00, -16.78, -5.45). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -46.99 -38.92 42.44 40.09 38.02 sized: 91.11 81.01 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.90% of box, grid points 102763 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 262 sec (No solvent overlap) Placed Na+ in aa at (18.19, -25.05, 2.58). (Replacing solvent molecule) Placed Cl- in aa at (20.19, -29.96, 3.04). (Replacing solvent molecule) Placed Na+ in aa at (21.45, -28.49, 5.85). (Replacing solvent molecule) Placed Cl- in aa at (23.66, -24.16, 5.79). (Replacing solvent molecule) Placed Na+ in aa at (23.87, -24.30, 0.65). (Replacing solvent molecule) Placed Cl- in aa at (24.98, -29.44, 2.89). (Replacing solvent molecule) Placed Na+ in aa at (26.24, -33.14, -7.39). (Replacing solvent molecule) Placed Cl- in aa at (39.87, 18.02, -3.44). (Replacing solvent molecule) Placed Na+ in aa at (41.94, 13.59, -3.09). (Replacing solvent molecule) Placed Cl- in aa at (43.46, 13.89, -5.66). (Replacing solvent molecule) Placed Na+ in aa at (42.38, 18.51, -4.69). (Replacing solvent molecule) Placed Cl- in aa at (12.79, 20.34, 10.16). (Replacing solvent molecule) Placed Na+ in aa at (8.99, 22.61, 13.44). (Replacing solvent molecule) Placed Cl- in aa at (6.87, 21.83, 10.28). (Replacing solvent molecule) Placed Na+ in aa at (9.37, 21.35, 7.96). (Replacing solvent molecule) Placed Cl- in aa at (6.22, 20.34, 15.91). (Replacing solvent molecule) Placed Na+ in aa at (14.21, 17.44, 14.04). (Replacing solvent molecule) Placed Cl- in aa at (18.03, 14.80, 17.79). (Replacing solvent molecule) Placed Na+ in aa at (23.19, -33.21, 0.72). (Replacing solvent molecule) Placed Cl- in aa at (25.83, -34.62, -1.31). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.81 -46.05 -38.42 51.25 41.51 38.10 sized: 94.19 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.89% of box, grid points 102455 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 199 sec (Replacing solvent molecule) Placed Na+ in aa at (-16.06, 13.88, 12.28). (Replacing solvent molecule) Placed Cl- in aa at (-9.09, 22.64, 18.66). (Replacing solvent molecule) Placed Na+ in aa at (-7.60, 29.82, 13.59). (Replacing solvent molecule) Placed Cl- in aa at (-18.18, -33.80, -6.36). (Replacing solvent molecule) Placed Na+ in aa at (-21.43, -34.02, -10.48). (Replacing solvent molecule) Placed Cl- in aa at (-22.16, -30.99, -13.21). (Replacing solvent molecule) Placed Na+ in aa at (-19.68, -36.22, -6.60). (Replacing solvent molecule) Placed Cl- in aa at (-22.55, -36.90, -8.66). (Replacing solvent molecule) Placed Na+ in aa at (-19.75, -25.78, -16.56). (Replacing solvent molecule) Placed Cl- in aa at (-23.18, -24.76, -18.76). (Replacing solvent molecule) Placed Na+ in aa at (-5.47, 25.09, 20.02). (Replacing solvent molecule) Placed Cl- in aa at (-4.12, 24.29, 24.10). (Replacing solvent molecule) Placed Na+ in aa at (-0.89, -40.12, -5.93). (Replacing solvent molecule) Placed Cl- in aa at (-10.59, 27.30, 16.07). (Replacing solvent molecule) Placed Na+ in aa at (-10.18, 25.24, 26.90). (Replacing solvent molecule) Placed Cl- in aa at (-1.50, 28.89, 21.07). (Replacing solvent molecule) Placed Na+ in aa at (-1.58, 25.42, 23.66). (Replacing solvent molecule) Placed Cl- in aa at (-1.67, -38.99, -1.80). (Replacing solvent molecule) Placed Na+ in aa at (-0.86, -39.93, 0.94). (Replacing solvent molecule) Placed Cl- in aa at (-1.13, -42.36, -1.55). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -50.15 -44.14 44.30 38.74 37.56 sized: 94.51 77.85 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.08% of box, grid points 106528 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 150 sec (No solvent overlap) Placed Na+ in aa at (-6.89, 19.01, 10.08). (Replacing solvent molecule) Placed Cl- in aa at (12.82, -35.90, -6.57). (Replacing solvent molecule) Placed Na+ in aa at (10.89, -31.91, -5.80). (Replacing solvent molecule) Placed Cl- in aa at (8.27, -31.58, -6.27). (Replacing solvent molecule) Placed Na+ in aa at (6.73, -31.87, -1.37). (Replacing solvent molecule) Placed Cl- in aa at (2.83, -39.46, 3.86). (Replacing solvent molecule) Placed Na+ in aa at (5.58, -39.39, 2.08). (Replacing solvent molecule) Placed Cl- in aa at (9.37, -32.21, -3.22). (Replacing solvent molecule) Placed Na+ in aa at (15.05, -37.72, -3.82). (No solvent overlap) Placed Cl- in aa at (18.11, -41.99, -2.92). (Replacing solvent molecule) Placed Na+ in aa at (15.59, -41.01, 2.15). (Replacing solvent molecule) Placed Cl- in aa at (14.26, -36.36, 0.26). (Replacing solvent molecule) Placed Na+ in aa at (17.40, -40.38, -7.44). (Replacing solvent molecule) Placed Cl- in aa at (17.64, -39.06, -10.78). (Replacing solvent molecule) Placed Na+ in aa at (15.52, -35.92, -13.81). (Replacing solvent molecule) Placed Cl- in aa at (11.07, -36.75, -12.80). (Replacing solvent molecule) Placed Na+ in aa at (10.65, -33.41, -16.62). (Replacing solvent molecule) Placed Cl- in aa at (11.11, -30.84, -20.72). (Replacing solvent molecule) Placed Na+ in aa at (9.95, -36.58, -8.63). (Replacing solvent molecule) Placed Cl- in aa at (3.25, -36.92, -10.52). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -49.78 -38.92 42.44 40.09 38.02 sized: 91.11 78.22 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.97% of box, grid points 104130 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 211 sec (Replacing solvent molecule) Placed Na+ in aa at (-13.32, 8.44, -13.97). (Replacing solvent molecule) Placed Cl- in aa at (-18.51, 13.72, -16.69). (Replacing solvent molecule) Placed Na+ in aa at (-12.07, -33.99, -7.37). (Replacing solvent molecule) Placed Cl- in aa at (-14.13, 3.57, -14.50). (Replacing solvent molecule) Placed Na+ in aa at (-13.31, 1.47, -12.97). (Replacing solvent molecule) Placed Cl- in aa at (-5.26, -40.34, -13.95). (Replacing solvent molecule) Placed Na+ in aa at (-7.41, -37.81, -14.11). (Replacing solvent molecule) Placed Cl- in aa at (-13.74, -33.82, -9.76). (Replacing solvent molecule) Placed Na+ in aa at (-16.03, -31.98, -14.10). (Replacing solvent molecule) Placed Cl- in aa at (-11.10, -41.23, -8.64). (Replacing solvent molecule) Placed Na+ in aa at (-9.13, -42.96, -9.54). (Replacing solvent molecule) Placed Cl- in aa at (-6.12, -44.99, -6.93). (Replacing solvent molecule) Placed Na+ in aa at (-5.66, -45.24, -2.79). (Replacing solvent molecule) Placed Cl- in aa at (-13.62, -0.66, -14.69). (Replacing solvent molecule) Placed Na+ in aa at (-17.21, 2.96, -13.29). (Replacing solvent molecule) Placed Cl- in aa at (10.16, -17.11, 8.15). (Replacing solvent molecule) Placed Na+ in aa at (12.59, -18.08, 7.40). (Replacing solvent molecule) Placed Cl- in aa at (17.45, -17.57, 5.97). (Replacing solvent molecule) Placed Na+ in aa at (19.51, -18.67, 2.59). (Replacing solvent molecule) Placed Cl- in aa at (22.66, -22.86, 3.64). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.75 -53.03 -39.43 43.98 40.06 40.13 sized: 92.25 74.97 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.07% of box, grid points 106223 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 145 sec (Replacing solvent molecule) Placed Na+ in aa at (-25.91, -9.91, -7.31). (Replacing solvent molecule) Placed Cl- in aa at (17.25, 20.21, 14.18). (Replacing solvent molecule) Placed Na+ in aa at (-14.66, 14.53, 14.75). (Replacing solvent molecule) Placed Cl- in aa at (-25.18, 11.19, 16.57). (Replacing solvent molecule) Placed Na+ in aa at (-25.74, 14.31, 12.42). (Replacing solvent molecule) Placed Cl- in aa at (-22.35, 18.39, 13.77). (Replacing solvent molecule) Placed Na+ in aa at (-27.74, 11.73, 21.26). (Replacing solvent molecule) Placed Cl- in aa at (-23.29, 10.85, 22.81). (Replacing solvent molecule) Placed Na+ in aa at (-20.24, 17.91, 15.77). (Replacing solvent molecule) Placed Cl- in aa at (-18.41, 14.62, 13.76). (Replacing solvent molecule) Placed Na+ in aa at (-21.82, 6.28, 24.19). (Replacing solvent molecule) Placed Cl- in aa at (-19.70, 6.49, 32.34). (Replacing solvent molecule) Placed Na+ in aa at (-19.49, 6.36, 27.20). (Replacing solvent molecule) Placed Cl- in aa at (27.31, -31.92, -11.06). (Replacing solvent molecule) Placed Na+ in aa at (-21.91, 2.17, 32.40). (Replacing solvent molecule) Placed Cl- in aa at (-23.10, 3.25, 26.77). (Replacing solvent molecule) Placed Na+ in aa at (-23.66, 10.64, 14.11). (Replacing solvent molecule) Placed Cl- in aa at (-28.10, 10.38, 11.37). (Replacing solvent molecule) Placed Na+ in aa at (-28.51, 6.39, 12.40). (Replacing solvent molecule) Placed Cl- in aa at (-29.15, 2.11, 14.04). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.94 -46.05 -38.42 51.25 41.51 40.19 sized: 91.06 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.10% of box, grid points 106976 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 237 sec (Replacing solvent molecule) Placed Na+ in aa at (-12.93, 8.47, -11.40). (Replacing solvent molecule) Placed Cl- in aa at (-11.96, 11.30, -14.83). (Replacing solvent molecule) Placed Na+ in aa at (-7.48, 11.48, -14.29). (Replacing solvent molecule) Placed Cl- in aa at (-4.02, 9.03, -17.11). (Replacing solvent molecule) Placed Na+ in aa at (-1.45, 10.79, -13.22). (Replacing solvent molecule) Placed Cl- in aa at (-5.35, 17.99, -16.32). (Replacing solvent molecule) Placed Na+ in aa at (-6.58, 16.21, -11.67). (Replacing solvent molecule) Placed Cl- in aa at (-2.81, 14.54, -14.86). (Replacing solvent molecule) Placed Na+ in aa at (-1.44, 21.12, -16.53). (Replacing solvent molecule) Placed Cl- in aa at (-2.50, 23.64, -14.14). (Replacing solvent molecule) Placed Na+ in aa at (-4.65, 21.47, -17.61). (Replacing solvent molecule) Placed Cl- in aa at (-8.43, 23.79, -17.03). (Replacing solvent molecule) Placed Na+ in aa at (-7.60, 29.82, -12.96). (Replacing solvent molecule) Placed Cl- in aa at (-5.22, 29.21, -14.27). (Replacing solvent molecule) Placed Na+ in aa at (-6.14, 25.08, -13.84). (Replacing solvent molecule) Placed Cl- in aa at (-10.59, 27.30, -10.48). (Replacing solvent molecule) Placed Na+ in aa at (-8.73, 30.93, -6.67). (Replacing solvent molecule) Placed Cl- in aa at (-7.43, 31.05, -1.00). (Replacing solvent molecule) Placed Na+ in aa at (0.51, 10.05, -20.35). (Replacing solvent molecule) Placed Cl- in aa at (1.72, 12.45, -19.32). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -50.15 -44.14 44.30 38.84 37.56 sized: 94.51 77.85 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.18% of box, grid points 108643 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 207 sec (No solvent overlap) Placed Na+ in aa at (4.11, -33.78, -5.92). (Replacing solvent molecule) Placed Cl- in aa at (5.61, -37.08, -6.06). (Replacing solvent molecule) Placed Na+ in aa at (6.21, -40.87, -0.60). (Replacing solvent molecule) Placed Cl- in aa at (8.37, -39.77, 2.58). (Replacing solvent molecule) Placed Na+ in aa at (11.77, -38.00, 3.50). (Replacing solvent molecule) Placed Cl- in aa at (10.18, -36.87, 5.87). (Replacing solvent molecule) Placed Na+ in aa at (1.75, -40.71, -4.13). (Replacing solvent molecule) Placed Cl- in aa at (-1.70, -38.67, -1.77). (Replacing solvent molecule) Placed Na+ in aa at (-1.55, -36.73, 3.83). (Replacing solvent molecule) Placed Cl- in aa at (4.76, -40.67, -4.49). (Replacing solvent molecule) Placed Na+ in aa at (10.11, -39.92, -5.26). (Replacing solvent molecule) Placed Cl- in aa at (12.54, -40.89, -6.01). (Replacing solvent molecule) Placed Na+ in aa at (-5.40, -36.46, -3.06). (Replacing solvent molecule) Placed Cl- in aa at (3.34, -41.86, -0.98). charges: 193 sec (Replacing solvent molecule) Placed Na+ in aa at (19.26, -24.63, 2.72). (Replacing solvent molecule) Placed Na+ in aa at (7.86, -38.97, 5.16). (Replacing solvent molecule) Placed Cl- in aa at (-9.76, 7.06, -14.91). (Replacing solvent molecule) Placed Cl- in aa at (9.47, -43.58, 8.36). (Replacing solvent molecule) Placed Na+ in aa at (-10.88, 5.37, -12.87). (Replacing solvent molecule) Placed Na+ in aa at (6.72, -43.64, 7.28). (Replacing solvent molecule) Placed Cl- in aa at (-7.37, 1.78, -12.88). (Replacing solvent molecule) Placed Cl- in aa at (12.77, -39.31, 5.65). (Replacing solvent molecule) Placed Na+ in aa at (-6.84, 8.47, -17.32). (Replacing solvent molecule) Placed Na+ in aa at (11.99, -39.64, 10.21). (Replacing solvent molecule) Placed Cl- in aa at (-7.77, 15.60, -18.07). (Replacing solvent molecule) Placed Cl- in aa at (0.98, -13.39, 23.80). Done adding ions. (Replacing solvent molecule) >Placed Na+ in aa at (-12.04, 18.65, -15.26). addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -51.43 -38.92 42.44 40.09 38.02 sized: 91.11 76.57 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 (Replacing solvent molecule) Placed Cl- in aa at (-10.94, 19.04, -12.30). (Replacing solvent molecule) Placed Na+ in aa at (-6.55, 16.34, -11.50). (Replacing solvent molecule) Placed Cl- in aa at (-5.02, 8.25, -20.09). (Replacing solvent molecule) Placed Na+ in aa at (13.43, -22.42, 6.20). (Replacing solvent molecule) Placed Cl- in aa at (15.40, -25.48, 5.89). (Replacing solvent molecule) Placed Na+ in aa at (20.19, -29.96, 3.04). (Replacing solvent molecule) Placed Cl- in aa at (18.53, -25.96, 7.12). (Replacing solvent molecule) Placed Na+ in aa at (13.47, -29.20, 6.48). (Replacing solvent molecule) Placed Cl- in aa at (19.07, -35.25, 3.60). grid build: 1 sec Volume = 5.02% of box, grid points 105373 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in aa at (15.41, -34.89, 4.33). (Replacing solvent molecule) Placed Cl- in aa at (10.58, -33.56, 4.64). (Replacing solvent molecule) Placed Na+ in aa at (7.91, -39.16, 5.29). (Replacing solvent molecule) Placed Cl- in aa at (8.42, -39.96, 2.72). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.75 -53.03 -39.43 43.98 40.06 40.13 sized: 92.25 74.97 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.14% of box, grid points 107772 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 167 sec (Replacing solvent molecule) Placed Na+ in aa at (-24.61, 6.83, 5.29). (Replacing solvent molecule) Placed Cl- in aa at (-28.23, 8.68, 1.77). (Replacing solvent molecule) Placed Na+ in aa at (-22.63, -2.54, 23.72). (Replacing solvent molecule) Placed Cl- in aa at (-25.75, 2.16, 7.42). (Replacing solvent molecule) Placed Na+ in aa at (-26.30, -2.66, 2.64). (Replacing solvent molecule) Placed Cl- in aa at (-24.28, -4.59, 30.15). (Replacing solvent molecule) Placed Na+ in aa at (-27.08, -1.13, 8.31). (Replacing solvent molecule) Placed Cl- in aa at (-28.98, -1.57, 5.58). (Replacing solvent molecule) Placed Na+ in aa at (-20.24, -5.09, 29.05). (Replacing solvent molecule) Placed Cl- in aa at (-20.81, -6.15, 24.41). (Replacing solvent molecule) Placed Na+ in aa at (-24.81, -6.28, 27.87). (Replacing solvent molecule) Placed Cl- in aa at (-25.32, -0.53, 17.79). (Replacing solvent molecule) Placed Na+ in aa at (-28.53, -1.57, 16.19). (Replacing solvent molecule) Placed Cl- in aa at (-25.16, -4.98, 9.84). (Replacing solvent molecule) Placed Na+ in aa at (-23.74, -6.73, 15.31). (Replacing solvent molecule) Placed Cl- in aa at (-25.33, -5.61, 17.97). (Replacing solvent molecule) Placed Na+ in aa at (-25.59, -6.59, 4.97). (Replacing solvent molecule) Placed Cl- in aa at (-28.05, -6.48, 2.81). (Replacing solvent molecule) Placed Na+ in aa at (-28.70, 4.33, 2.15). (Replacing solvent molecule) Placed Cl- in aa at (-27.07, 1.61, 1.30). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.94 -46.05 -38.42 51.25 41.51 40.19 sized: 91.06 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.17% of box, grid points 108323 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 216 sec (Replacing solvent molecule) Placed Na+ in aa at (-3.51, -43.43, -3.61). (Replacing solvent molecule) Placed Cl- in aa at (-9.42, 33.11, -10.95). (Replacing solvent molecule) Placed Na+ in aa at (-5.64, 33.07, -10.63). (Replacing solvent molecule) Placed Cl- in aa at (-6.38, 33.79, -6.44). (Replacing solvent molecule) Placed Na+ in aa at (-5.97, 35.55, -8.99). (Replacing solvent molecule) Placed Cl- in aa at (-4.46, 35.41, -12.54). (Replacing solvent molecule) Placed Na+ in aa at (-9.06, 35.62, -4.16). (Replacing solvent molecule) Placed Cl- in aa at (-12.42, 24.38, 29.61). (Replacing solvent molecule) Placed Na+ in aa at (-11.45, 20.86, 33.10). (Replacing solvent molecule) Placed Cl- in aa at (-13.29, 21.23, 29.10). (Replacing solvent molecule) Placed Na+ in aa at (-9.56, 17.46, 27.42). (Replacing solvent molecule) Placed Cl- in aa at (-11.10, 17.37, 32.24). (Replacing solvent molecule) Placed Na+ in aa at (-7.80, 15.47, 34.86). (Replacing solvent molecule) Placed Cl- in aa at (-8.68, 21.56, 27.04). (Replacing solvent molecule) Placed Na+ in aa at (-17.42, 23.88, 28.16). (Replacing solvent molecule) Placed Cl- in aa at (-11.73, 13.53, 33.90). (Replacing solvent molecule) Placed Na+ in aa at (-14.09, 14.32, 32.93). (Replacing solvent molecule) Placed Cl- in aa at (-8.49, 19.04, 32.68). (Replacing solvent molecule) Placed Na+ in aa at (-6.15, 23.86, 32.73). (Replacing solvent molecule) Placed Cl- in aa at (-2.63, 25.94, 29.98). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -51.22 -44.14 44.30 43.41 42.65 sized: 94.51 76.78 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.35% of box, grid points 112294 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 196 sec (Replacing solvent molecule) Placed Na+ in aa at (24.64, 6.45, 14.58). (Replacing solvent molecule) Placed Cl- in aa at (27.07, 9.46, 14.43). (Replacing solvent molecule) Placed Na+ in aa at (30.62, 7.47, 13.30). (Replacing solvent molecule) Placed Cl- in aa at (31.51, 5.31, 10.30). (Replacing solvent molecule) Placed Na+ in aa at (31.97, 8.79, 8.27). (Replacing solvent molecule) Placed Cl- in aa at (31.64, 11.45, 16.43). (Replacing solvent molecule) Placed Na+ in aa at (27.26, 14.26, 15.36). (Replacing solvent molecule) Placed Cl- in aa at (34.69, 12.07, 11.75). (Replacing solvent molecule) Placed Na+ in aa at (34.66, 14.21, 13.79). (Replacing solvent molecule) Placed Cl- in aa at (30.00, 16.99, 13.44). (Replacing solvent molecule) Placed Na+ in aa at (32.90, 16.92, 10.88). (Replacing solvent molecule) Placed Cl- in aa at (34.49, 17.75, 6.70). (Replacing solvent molecule) Placed Na+ in aa at (34.24, 15.29, 5.41). (Replacing solvent molecule) Placed Cl- in aa at (31.78, 13.73, 8.02). (Replacing solvent molecule) Placed Na+ in aa at (30.17, 17.93, 6.94). (Replacing solvent molecule) Placed Cl- in aa at (29.95, 22.07, 7.00). (Replacing solvent molecule) Placed Na+ in aa at (-20.70, 1.94, 23.80). (Replacing solvent molecule) Placed Cl- in aa at (-21.81, -3.51, 30.86). (Replacing solvent molecule) Placed Na+ in aa at (-20.29, -4.90, 28.91). (Replacing solvent molecule) Placed Cl- in aa at (-22.68, -2.36, 23.58). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.89 -51.43 -38.92 42.48 40.09 38.65 sized: 91.11 76.57 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 charges: 197 sec (No solvent overlap) Placed Na+ in aa at (-9.75, 3.97, 28.57). (Replacing solvent molecule) Placed Cl- in aa at (-11.52, -1.79, 34.71). (Replacing solvent molecule) Placed Na+ in aa at (-13.62, -0.66, 38.41). charges: 172 sec (Replacing solvent molecule) Placed Na+ in aa at (30.05, 2.67, 7.92). (Replacing solvent molecule) Placed Cl- in aa at (18.45, -31.54, 6.55). (Replacing solvent molecule) Placed Cl- in aa at (31.56, 5.12, 10.44). (Replacing solvent molecule) Placed Na+ in aa at (-13.64, -4.99, 32.66). (Replacing solvent molecule) Placed Na+ in aa at (33.16, 2.96, 8.28). (Replacing solvent molecule) Placed Cl- in aa at (-16.87, -2.54, 35.47). (Replacing solvent molecule) Placed Cl- in aa at (30.15, 0.02, 6.01). grid build: 1 sec Volume = 5.16% of box, grid points 108126 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in aa at (21.58, -30.60, 9.44). (Replacing solvent molecule) Placed Na+ in aa at (28.53, -0.93, 2.64). (Replacing solvent molecule) Placed Cl- in aa at (-6.26, -0.40, 27.16). (Replacing solvent molecule) Placed Cl- in aa at (35.53, -1.40, 1.44). (Replacing solvent molecule) Placed Na+ in aa at (-5.68, -5.01, 30.19). (Replacing solvent molecule) Placed Na+ in aa at (28.29, -2.24, 5.97). (Replacing solvent molecule) Placed Cl- in aa at (-10.84, -8.68, 30.45). (Replacing solvent molecule) Placed Cl- in aa at (34.65, 0.40, -6.50). (Replacing solvent molecule) Placed Na+ in aa at (-9.06, -0.23, 32.10). (Replacing solvent molecule) Placed Na+ in aa at (33.60, -0.61, -1.63). (Replacing solvent molecule) Placed Cl- in aa at (-4.23, -2.24, 32.52). (Replacing solvent molecule) Placed Cl- in aa at (29.77, -4.55, 6.51). (Replacing solvent molecule) Placed Na+ in aa at (-4.06, -1.40, 25.31). (Replacing solvent molecule) Placed Na+ in aa at (32.37, -2.94, 10.07). (Replacing solvent molecule) Placed Cl- in aa at (-2.17, -3.34, 29.14). (Replacing solvent molecule) Placed Cl- in aa at (35.29, 0.99, 9.31). (Replacing solvent molecule) Placed Na+ in aa at (1.71, -4.64, 30.28). (Replacing solvent molecule) Placed Na+ in aa at (37.10, 2.73, 4.90). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (1.08, -0.61, 24.92). Placed Cl- in aa at (40.93, 6.03, 2.72). (Replacing solvent molecule) Placed Na+ in aa at (0.69, -5.29, 27.07). (Replacing solvent molecule) Placed Na+ in aa at (37.33, 5.13, -4.36). (Replacing solvent molecule) Placed Cl- in aa at (-5.21, -8.92, 28.77). (Replacing solvent molecule) Placed Cl- in aa at (33.59, 3.39, 2.35). (Replacing solvent molecule) Placed Na+ in aa at (-3.65, 2.06, 31.24). (Replacing solvent molecule) Placed Na+ in aa at (38.78, 4.93, -0.46). (Replacing solvent molecule) Placed Cl- in aa at (-2.07, 0.93, 28.59). (Replacing solvent molecule) Placed Cl- in aa at (41.40, 3.16, -4.44). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid (Replacing solvent molecule) Placed Na+ in aa at (42.67, 5.88, -5.12). Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.75 -53.03 -39.43 43.98 40.06 46.20 sized: 92.25 74.97 88.57 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 (Replacing solvent molecule) Placed Cl- in aa at (30.82, -1.10, 11.00). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.94 -46.05 -38.42 51.25 41.51 40.19 sized: 91.06 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.27% of box, grid points 110522 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges grid build: 1 sec Volume = 5.26% of box, grid points 110325 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 176 sec (Replacing solvent molecule) Placed Na+ in aa at (-16.99, -11.99, 11.72). (Replacing solvent molecule) Placed Cl- in aa at (-21.04, -12.77, 13.65). (Replacing solvent molecule) Placed Na+ in aa at (-20.65, -8.09, 11.51). (Replacing solvent molecule) Placed Cl- in aa at (-20.66, -4.08, 15.49). (Replacing solvent molecule) Placed Na+ in aa at (-18.95, -6.49, 22.45). (Replacing solvent molecule) Placed Cl- in aa at (-18.72, -8.88, 14.58). (Replacing solvent molecule) Placed Na+ in aa at (-19.10, -6.02, 19.62). (Replacing solvent molecule) Placed Cl- in aa at (-22.19, -7.68, 26.65). (Replacing solvent molecule) Placed Na+ in aa at (-19.60, -7.08, 33.19). (Replacing solvent molecule) Placed Cl- in aa at (-24.20, -4.81, 21.05). (Replacing solvent molecule) Placed Na+ in aa at (-25.38, -5.42, 17.83). (Replacing solvent molecule) Placed Cl- in aa at (-18.20, -10.49, 33.50). (Replacing solvent molecule) Placed Na+ in aa at (-25.83, -6.06, 24.13). (Replacing solvent molecule) Placed Cl- in aa at (-17.63, -15.47, 11.95). (Replacing solvent molecule) Placed Na+ in aa at (-21.87, -16.52, 10.78). (Replacing solvent molecule) Placed Cl- in aa at (-16.29, -8.60, 21.44). (Replacing solvent molecule) Placed Na+ in aa at (-18.40, -12.10, 30.38). (Replacing solvent molecule) Placed Cl- in aa at (14.78, 13.94, 16.05). (Replacing solvent molecule) Placed Na+ in aa at (-15.87, -10.98, 19.69). (Replacing solvent molecule) Placed Cl- in aa at (-16.54, -14.39, 23.63). Done adding ions. > > saveamberparm aa m2.topo m2.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 15057 ) (no restraints) > > quit Quit charges: 213 sec (No solvent overlap) Placed Na+ in aa at (-2.49, 7.78, -0.14). (Replacing solvent molecule) Placed Cl- in aa at (-21.85, 6.15, 24.02). (Replacing solvent molecule) Placed Na+ in aa at (-19.39, 10.16, 22.64). (Replacing solvent molecule) Placed Cl- in aa at (-2.55, 21.75, -19.58). (Replacing solvent molecule) Placed Na+ in aa at (-6.29, 26.30, -22.38). (Replacing solvent molecule) Placed Cl- in aa at (-19.68, 9.77, 19.95). (Replacing solvent molecule) Placed Na+ in aa at (-19.52, 6.23, 27.04). (Replacing solvent molecule) Placed Cl- in aa at (-17.60, 7.21, 25.20). (Replacing solvent molecule) Placed Na+ in aa at (-12.42, 10.09, 23.66). (Replacing solvent molecule) Placed Cl- in aa at (-12.34, 13.56, 21.07). (Replacing solvent molecule) Placed Na+ in aa at (-14.86, 16.69, 22.71). (Replacing solvent molecule) Placed Cl- in aa at (-17.21, 18.46, 20.11). (Replacing solvent molecule) Placed Na+ in aa at (-18.46, 22.57, 24.36). (Replacing solvent molecule) Placed Cl- in aa at (-13.65, 22.21, 24.97). (Replacing solvent molecule) Placed Na+ in aa at (-14.16, 20.67, 18.82). (Replacing solvent molecule) Placed Cl- in aa at (-16.13, 13.19, 25.71). (Replacing solvent molecule) Placed Na+ in aa at (-14.00, 8.92, 27.70). (Replacing solvent molecule) Placed Cl- in aa at (-21.81, 26.57, 27.36). (Replacing solvent molecule) Placed Na+ in aa at (-3.83, 21.80, -23.76). (Replacing solvent molecule) Placed Cl- in aa at (-6.40, 24.05, -23.91). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.49 -51.22 -44.14 44.30 43.41 42.65 sized: 94.51 76.78 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.42% of box, grid points 113582 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 200 sec (Replacing solvent molecule) Placed Na+ in aa at (-27.03, 1.67, 10.35). (Replacing solvent molecule) Placed Cl- in aa at (40.07, 5.47, -7.56). (Replacing solvent molecule) Placed Na+ in aa at (38.93, 4.88, -12.37). (Replacing solvent molecule) Placed Cl- in aa at (35.82, 8.88, -10.39). (Replacing solvent molecule) Placed Na+ in aa at (37.31, 12.45, -10.99). (Replacing solvent molecule) Placed Cl- in aa at (41.38, 10.64, -12.44). (Replacing solvent molecule) Placed Na+ in aa at (42.29, 14.51, -10.33). (Replacing solvent molecule) Placed Cl- in aa at (37.24, 16.33, -6.93). (Replacing solvent molecule) Placed Na+ in aa at (35.99, 17.11, -12.88). (Replacing solvent molecule) Placed Cl- in aa at (33.50, 15.46, -9.64). (Replacing solvent molecule) Placed Na+ in aa at (32.26, 20.09, -8.64). (Replacing solvent molecule) Placed Cl- in aa at (43.28, 19.29, -8.83). (Replacing solvent molecule) Placed Na+ in aa at (39.54, 22.20, 1.48). (Replacing solvent molecule) Placed Cl- in aa at (38.52, 8.43, -8.76). (Replacing solvent molecule) Placed Na+ in aa at (37.41, 5.01, -8.83). (Replacing solvent molecule) Placed Cl- in aa at (35.53, 21.59, -11.83). (Replacing solvent molecule) Placed Na+ in aa at (39.34, 22.99, -9.62). (Replacing solvent molecule) Placed Cl- in aa at (40.09, 24.55, -1.04). (Replacing solvent molecule) Placed Na+ in aa at (42.52, 9.22, -8.49). (Replacing solvent molecule) Placed Cl- in aa at (39.29, 25.15, -5.86). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -36.94 -46.05 -38.42 51.25 41.51 40.19 sized: 91.06 81.95 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.35% of box, grid points 112231 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 208 sec (No solvent overlap) Placed Na+ in aa at (-11.75, 14.97, 12.57). (Replacing solvent molecule) Placed Cl- in aa at (-16.19, 17.00, 10.35). (Replacing solvent molecule) Placed Na+ in aa at (-12.16, 17.55, 8.49). (Replacing solvent molecule) Placed Cl- in aa at (-12.04, 18.65, 11.30). (Replacing solvent molecule) Placed Na+ in aa at (-16.45, 17.87, 16.09). (Replacing solvent molecule) Placed Cl- in aa at (4.47, -6.48, 29.36). (Replacing solvent molecule) Placed Na+ in aa at (6.93, -6.59, 31.52). (Replacing solvent molecule) Placed Cl- in aa at (-20.24, 17.91, 15.77). (Replacing solvent molecule) Placed Na+ in aa at (-18.41, 14.62, 13.76). (Replacing solvent molecule) Placed Cl- in aa at (-17.69, 13.76, 16.19). (Replacing solvent molecule) Placed Na+ in aa at (-20.81, 16.85, 11.13). (Replacing solvent molecule) Placed Cl- in aa at (-21.82, 12.39, 10.07). (Replacing solvent molecule) Placed Na+ in aa at (-27.34, 7.57, 14.67). (Replacing solvent molecule) Placed Cl- in aa at (-27.58, 7.70, 9.91). (Replacing solvent molecule) Placed Na+ in aa at (-23.87, 10.31, 9.81). (Replacing solvent molecule) Placed Cl- in aa at (4.77, -11.27, 34.53). (Replacing solvent molecule) Placed Na+ in aa at (2.44, -6.74, 36.24). (Replacing solvent molecule) Placed Cl- in aa at (-2.19, -5.02, 36.36). (Replacing solvent molecule) Placed Na+ in aa at (-3.76, 0.35, 34.80). (Replacing solvent molecule) Placed Cl- in aa at (-5.45, 2.22, 33.46). Done adding ions. > > saveamberparm aa m4.topo m4.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14444 ) (no restraints) > > quit Quit charges: 161 sec (Replacing solvent molecule) Placed Na+ in aa at (38.38, 19.49, -6.72). (Replacing solvent molecule) Placed Cl- in aa at (39.29, 14.31, -14.13). (Replacing solvent molecule) Placed Na+ in aa at (34.29, 15.10, -21.00). (Replacing solvent molecule) Placed Cl- in aa at (34.54, 17.56, -19.71). (Replacing solvent molecule) Placed Na+ in aa at (30.91, 18.52, -17.02). (Replacing solvent molecule) Placed Cl- in aa at (30.22, 17.74, -19.47). (Replacing solvent molecule) Placed Na+ in aa at (32.79, 19.76, -23.59). (No solvent overlap) Placed Cl- in aa at (45.06, 8.95, -5.42). (Replacing solvent molecule) Placed Na+ in aa at (36.93, 10.38, -15.18). (Replacing solvent molecule) Placed Cl- in aa at (34.27, 12.57, -19.15). (Replacing solvent molecule) Placed Na+ in aa at (35.11, 8.24, -20.35). (Replacing solvent molecule) Placed Cl- in aa at (40.21, 4.70, -19.43). (Replacing solvent molecule) Placed Na+ in aa at (39.71, 6.28, -17.24). (Replacing solvent molecule) Placed Cl- in aa at (37.98, 8.78, -20.25). (Replacing solvent molecule) Placed Na+ in aa at (37.11, 13.31, -18.29). (Replacing solvent molecule) Placed Cl- in aa at (34.47, 5.01, -16.39). (Replacing solvent molecule) Placed Na+ in aa at (33.55, 9.42, -15.89). (Replacing solvent molecule) Placed Cl- in aa at (34.74, 11.88, -14.67). (Replacing solvent molecule) Placed Na+ in aa at (32.37, 13.95, -15.64). (Replacing solvent molecule) Placed Cl- in aa at (37.70, 16.08, -29.34). Done adding ions. > > saveamberparm aa m1.topo m1.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. charges: 174 sec Building bond parameters. (No solvent overlap) Placed Na+ in aa at (24.51, -16.22, -11.14). (Replacing solvent molecule) Placed Cl- in aa at (26.38, -20.90, -13.84). Building angle parameters. Building proper torsion parameters. (Replacing solvent molecule) Placed Na+ in aa at (24.09, -22.19, -17.03). (Replacing solvent molecule) Placed Cl- in aa at (21.07, -25.13, -20.00). (Replacing solvent molecule) Placed Na+ in aa at (24.13, -25.51, -14.01). (Replacing solvent molecule) Placed Cl- in aa at (21.55, -27.08, -12.47). (Replacing solvent molecule) Placed Na+ in aa at (15.37, -25.60, -20.83). (Replacing solvent molecule) Placed Cl- in aa at (16.45, -24.38, -24.50). (Replacing solvent molecule) Placed Na+ in aa at (27.09, -16.58, -18.41). (Replacing solvent molecule) Placed Cl- in aa at (23.87, -18.37, -19.22). (Replacing solvent molecule) Placed Na+ in aa at (21.97, -15.82, -20.75). Building improper torsion parameters. (Replacing solvent molecule) ** Warning: No sp2 improper torsion term for C*-CN-CB-CA Placed Cl- in aa at (18.00, -13.40, -22.03). atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. (Replacing solvent molecule) Placed Na+ in aa at (20.45, -27.47, -15.42). Not Marking per-residue atom chain types. (Replacing solvent molecule) Marking per-residue atom chain types. Placed Cl- in aa at (14.97, -27.09, -14.75). (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14439 ) (no restraints) (No solvent overlap) Placed Na+ in aa at (11.51, -27.22, -13.14). (Replacing solvent molecule) Placed Cl- in aa at (27.87, -24.52, -17.61). (Replacing solvent molecule) Placed Na+ in aa at (11.46, -27.83, -18.44). (Replacing solvent molecule) Placed Cl- in aa at (10.14, -30.47, -17.85). (Replacing solvent molecule) Placed Na+ in aa at (7.05, -30.44, -18.47). (Replacing solvent molecule) Placed Cl- in aa at (6.75, -31.81, -14.29). Done adding ions. > > saveamberparm aa m3.topo m3.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. >Building bond parameters. > quit Quit Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 15296 ) (no restraints) > > quit Quit log started: Fri Aug 1 16:30:04 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m1.pdb Loading PDB file: ./m1.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m1_invacuo.topo m1_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.363324 to meet diagonal cut criterion Solute vdw bounding box: 49.450 66.410 71.273 Total bounding box for atom centers: 103.993 103.993 103.993 (box expansion for 'iso' is 32.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 578693.992 A^3 (oct) Total mass 315257.842 amu, Density 0.905 g/cc Added 14577 residues. > > addions aa Na+ 0 6 Na+ ions required to neutralize. Adding 6 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -33.34 -40.88 -37.95 41.42 39.54 37.63 sized: 94.66 87.12 90.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.10% of box, grid points 86062 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Fri Aug 1 16:31:00 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m2.pdb Loading PDB file: ./m2.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m2_invacuo.topo m2_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.379597 to meet diagonal cut criterion Solute vdw bounding box: 50.614 66.247 72.160 Total bounding box for atom centers: 105.271 105.271 105.271 (box expansion for 'iso' is 33.2%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 600078.753 A^3 (oct) Total mass 326319.666 amu, Density 0.903 g/cc Added 15191 residues. > > addions aa Na+ 0 6 Na+ ions required to neutralize. Adding 6 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -33.22 -41.31 -38.45 41.97 38.17 37.55 sized: 94.78 86.69 89.55 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.08% of box, grid points 85635 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Fri Aug 1 16:31:16 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m3.pdb Loading PDB file: ./m3.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m3_invacuo.topo m3_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.450544 to meet diagonal cut criterion Solute vdw bounding box: 52.146 67.004 71.089 Total bounding box for atom centers: 105.902 105.902 105.902 (box expansion for 'iso' is 26.7%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 610837.974 A^3 (oct) Total mass 330643.506 amu, Density 0.899 g/cc Added 15431 residues. > > addions aa Na+ 0 6 Na+ ions required to neutralize. Adding 6 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.22 -43.51 -43.67 43.83 38.27 37.09 sized: 95.78 84.49 84.33 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.23% of box, grid points 88701 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Fri Aug 1 16:31:33 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m4.pdb Loading PDB file: ./m4.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m4_invacuo.topo m4_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.419079 to meet diagonal cut criterion Solute vdw bounding box: 47.880 66.283 69.913 Total bounding box for atom centers: 103.971 103.971 103.971 (box expansion for 'iso' is 31.5%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 578325.028 A^3 (oct) Total mass 315311.890 amu, Density 0.905 g/cc Added 14580 residues. > > addions aa Na+ 0 6 Na+ ions required to neutralize. Adding 6 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.92 -42.12 -38.26 43.51 39.59 37.38 sized: 95.08 85.88 89.74 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.04% of box, grid points 84805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 94 sec (Replacing solvent molecule) Placed Na+ in aa at (25.05, -13.22, -12.51). (Replacing solvent molecule) Placed Na+ in aa at (30.05, 2.67, 7.92). (Replacing solvent molecule) Placed Na+ in aa at (-0.23, -36.16, -7.42). (Replacing solvent molecule) Placed Na+ in aa at (20.12, -21.48, 3.23). (Replacing solvent molecule) Placed Na+ in aa at (-26.17, -11.16, -0.32). (Replacing solvent molecule) Placed Na+ in aa at (-14.66, 14.53, 14.75). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -33.49 -43.48 -37.95 41.42 39.54 37.63 sized: 94.51 84.52 90.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.15% of box, grid points 87059 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges log started: Fri Aug 1 16:32:01 2008 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0181375/AMBER/amber9/opteron-pathscale-serial-static/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./buildit > > #CM5 = loadmol2 cm5.mol2 > #TMI = loadmol2 tmi.mol2 > loadoff heme.off Loading library: ./heme.off Loading: HEM > gaff = loadamberparams gaff.dat Loading parameters: ./gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > heme = loadamberparams hemes3.frcmod Loading parameters: ./hemes3.frcmod Reading force field modification type file (frcmod) Reading title: fe+3 heme: p450-o2 heme-no Unknown keyword: in parameter file. WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X hy c4 X 1 0.000 180.000 2.000 WARNING: expected Improper Torsion PK>0 (0.000000) Here is the Improper Torsion line in question: X cf hz X 1 0.000 180.000 2.000 (UNKNOWN ATOM TYPE: lo) (UNKNOWN ATOM TYPE: lw) (UNKNOWN ATOM TYPE: o5) (UNKNOWN ATOM TYPE: lc) (UNKNOWN ATOM TYPE: ln) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: c5) (UNKNOWN ATOM TYPE: c4) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: he) (UNKNOWN ATOM TYPE: hm) (UNKNOWN ATOM TYPE: hk) (UNKNOWN ATOM TYPE: hj) (UNKNOWN ATOM TYPE: hy) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hz) (UNKNOWN ATOM TYPE: lh) > ions = loadamberparams frcmod_smith_dang Loading parameters: ./frcmod_smith_dang Reading force field modification type file (frcmod) Reading title: smith/dang ion parameters (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: IP) > loadoff CYP.off Loading library: ./CYP.off Loading: CYP > > > aa = loadpdb m5.pdb Loading PDB file: ./m5.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PRO, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: PRO, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: ASN, Nonterminal, was not found in name map.) (Residue 12: LEU, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: HIS, Nonterminal, was not found in name map.) (Residue 15: VAL, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: PHE, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: PRO, Nonterminal, was not found in name map.) (Residue 22: TYR, Nonterminal, was not found in name map.) (Residue 23: CYS, Nonterminal, was not found in name map.) (Residue 24: PHE, Nonterminal, was not found in name map.) (Residue 25: ASP, Nonterminal, was not found in name map.) (Residue 26: GLN, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ARG, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: ARG, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: VAL, Nonterminal, was not found in name map.) (Residue 35: PHE, Nonterminal, was not found in name map.) (Residue 36: SER, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: TRP, Nonterminal, was not found in name map.) (Residue 42: THR, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: VAL, Nonterminal, was not found in name map.) (Residue 46: VAL, Nonterminal, was not found in name map.) (Residue 47: LEU, Nonterminal, was not found in name map.) (Residue 48: ASN, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: ALA, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: ARG, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ALA, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: THR, Nonterminal, was not found in name map.) (Residue 60: HIS, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: GLU, Nonterminal, was not found in name map.) (Residue 63: ASP, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: ALA, Nonterminal, was not found in name map.) (Residue 66: ASP, Nonterminal, was not found in name map.) (Residue 67: ARG, Nonterminal, was not found in name map.) (Residue 68: PRO, Nonterminal, was not found in name map.) (Residue 69: PRO, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: ILE, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: GLN, Nonterminal, was not found in name map.) (Residue 75: ILE, Nonterminal, was not found in name map.) (Residue 76: LEU, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: PHE, Nonterminal, was not found in name map.) (Residue 79: GLY, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: GLN, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: PHE, Nonterminal, was not found in name map.) (Residue 87: LEU, Nonterminal, was not found in name map.) (Residue 88: ALA, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: GLY, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: TRP, Nonterminal, was not found in name map.) (Residue 95: ARG, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLN, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: ARG, Nonterminal, was not found in name map.) (Residue 100: PHE, Nonterminal, was not found in name map.) (Residue 101: SER, Nonterminal, was not found in name map.) (Residue 102: VAL, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: THR, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: ASN, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLY, Nonterminal, was not found in name map.) (Residue 112: LYS, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LEU, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: GLN, Nonterminal, was not found in name map.) (Residue 118: TRP, Nonterminal, was not found in name map.) (Residue 119: VAL, Nonterminal, was not found in name map.) (Residue 120: THR, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: ALA, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: CYS, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: CYS, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ALA, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: SER, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ARG, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: ASN, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: LEU, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: LYS, Nonterminal, was not found in name map.) (Residue 147: ALA, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ASN, Nonterminal, was not found in name map.) (Residue 151: VAL, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: SER, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: CYS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: ARG, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: TYR, Nonterminal, was not found in name map.) (Residue 164: ASP, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: PRO, Nonterminal, was not found in name map.) (Residue 167: ARG, Nonterminal, was not found in name map.) (Residue 168: PHE, Nonterminal, was not found in name map.) (Residue 169: LEU, Nonterminal, was not found in name map.) (Residue 170: ARG, Nonterminal, was not found in name map.) (Residue 171: LEU, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: LEU, Nonterminal, was not found in name map.) (Residue 175: ALA, Nonterminal, was not found in name map.) (Residue 176: GLN, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: GLY, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: LEU, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: GLU, Nonterminal, was not found in name map.) (Residue 189: VAL, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: ALA, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ASP, Nonterminal, was not found in name map.) (Residue 197: ARG, Nonterminal, was not found in name map.) (Residue 198: HIS, Nonterminal, was not found in name map.) (Residue 199: ILE, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: ALA, Nonterminal, was not found in name map.) (Residue 202: LEU, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: LEU, Nonterminal, was not found in name map.) (Residue 208: ARG, Nonterminal, was not found in name map.) (Residue 209: PHE, Nonterminal, was not found in name map.) (Residue 210: GLN, Nonterminal, was not found in name map.) (Residue 211: LYS, Nonterminal, was not found in name map.) (Residue 212: ALA, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: LEU, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLN, Nonterminal, was not found in name map.) (Residue 217: LEU, Nonterminal, was not found in name map.) (Residue 218: ASP, Nonterminal, was not found in name map.) (Residue 219: GLU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: THR, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: HIS, Nonterminal, was not found in name map.) (Residue 225: ARG, Nonterminal, was not found in name map.) (Residue 226: MET, Nonterminal, was not found in name map.) (Residue 227: THR, Nonterminal, was not found in name map.) (Residue 228: TRP, Nonterminal, was not found in name map.) (Residue 229: ASP, Nonterminal, was not found in name map.) (Residue 230: PRO, Nonterminal, was not found in name map.) (Residue 231: ALA, Nonterminal, was not found in name map.) (Residue 232: GLN, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: ARG, Nonterminal, was not found in name map.) (Residue 236: ASP, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: THR, Nonterminal, was not found in name map.) (Residue 239: GLU, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: PHE, Nonterminal, was not found in name map.) (Residue 242: LEU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: GLU, Nonterminal, was not found in name map.) (Residue 245: MET, Nonterminal, was not found in name map.) (Residue 246: GLU, Nonterminal, was not found in name map.) (Residue 247: LYS, Nonterminal, was not found in name map.) (Residue 248: ALA, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: GLY, Nonterminal, was not found in name map.) (Residue 251: ASN, Nonterminal, was not found in name map.) (Residue 252: PRO, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: SER, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: ASN, Nonterminal, was not found in name map.) (Residue 258: ASP, Nonterminal, was not found in name map.) (Residue 259: GLU, Nonterminal, was not found in name map.) (Residue 260: ASN, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: ARG, Nonterminal, was not found in name map.) (Residue 263: ILE, Nonterminal, was not found in name map.) (Residue 264: VAL, Nonterminal, was not found in name map.) (Residue 265: VAL, Nonterminal, was not found in name map.) (Residue 266: ALA, Nonterminal, was not found in name map.) (Residue 267: ASP, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: PHE, Nonterminal, was not found in name map.) (Residue 270: SER, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: GLY, Nonterminal, was not found in name map.) (Residue 273: MET, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: THR, Nonterminal, was not found in name map.) (Residue 279: THR, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: ALA, Nonterminal, was not found in name map.) (Residue 282: TRP, Nonterminal, was not found in name map.) (Residue 283: GLY, Nonterminal, was not found in name map.) (Residue 284: LEU, Nonterminal, was not found in name map.) (Residue 285: LEU, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: MET, Nonterminal, was not found in name map.) (Residue 288: ILE, Nonterminal, was not found in name map.) (Residue 289: LEU, Nonterminal, was not found in name map.) (Residue 290: HIS, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ASP, Nonterminal, was not found in name map.) (Residue 293: VAL, Nonterminal, was not found in name map.) (Residue 294: GLN, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: ARG, Nonterminal, was not found in name map.) (Residue 297: VAL, Nonterminal, was not found in name map.) (Residue 298: GLN, Nonterminal, was not found in name map.) (Residue 299: GLN, Nonterminal, was not found in name map.) (Residue 300: GLU, Nonterminal, was not found in name map.) (Residue 301: ILE, Nonterminal, was not found in name map.) (Residue 302: ASP, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: VAL, Nonterminal, was not found in name map.) (Residue 305: ILE, Nonterminal, was not found in name map.) (Residue 306: GLY, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: ARG, Nonterminal, was not found in name map.) (Residue 310: ARG, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: MET, Nonterminal, was not found in name map.) (Residue 314: GLY, Nonterminal, was not found in name map.) (Residue 315: ASP, Nonterminal, was not found in name map.) (Residue 316: GLN, Nonterminal, was not found in name map.) (Residue 317: ALA, Nonterminal, was not found in name map.) (Residue 318: HIS, Nonterminal, was not found in name map.) (Residue 319: MET, Nonterminal, was not found in name map.) (Residue 320: PRO, Nonterminal, was not found in name map.) (Residue 321: TYR, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: THR, Nonterminal, was not found in name map.) (Residue 324: ALA, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: HIS, Nonterminal, was not found in name map.) (Residue 328: GLU, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: GLN, Nonterminal, was not found in name map.) (Residue 331: ARG, Nonterminal, was not found in name map.) (Residue 332: PHE, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: ASP, Nonterminal, was not found in name map.) (Residue 335: ILE, Nonterminal, was not found in name map.) (Residue 336: VAL, Nonterminal, was not found in name map.) (Residue 337: PRO, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: GLY, Nonterminal, was not found in name map.) (Residue 340: MET, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: HIS, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: SER, Nonterminal, was not found in name map.) (Residue 346: ARG, Nonterminal, was not found in name map.) (Residue 347: ASP, Nonterminal, was not found in name map.) (Residue 348: ILE, Nonterminal, was not found in name map.) (Residue 349: GLU, Nonterminal, was not found in name map.) (Residue 350: VAL, Nonterminal, was not found in name map.) (Residue 351: GLN, Nonterminal, was not found in name map.) (Residue 352: GLY, Nonterminal, was not found in name map.) (Residue 353: PHE, Nonterminal, was not found in name map.) (Residue 354: ARG, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: PRO, Nonterminal, was not found in name map.) (Residue 357: LYS, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: THR, Nonterminal, was not found in name map.) (Residue 360: THR, Nonterminal, was not found in name map.) (Residue 361: LEU, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: THR, Nonterminal, was not found in name map.) (Residue 364: ASN, Nonterminal, was not found in name map.) (Residue 365: LEU, Nonterminal, was not found in name map.) (Residue 366: SER, Nonterminal, was not found in name map.) (Residue 367: SER, Nonterminal, was not found in name map.) (Residue 368: VAL, Nonterminal, was not found in name map.) (Residue 369: LEU, Nonterminal, was not found in name map.) (Residue 370: LYS, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: GLU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: TRP, Nonterminal, was not found in name map.) (Residue 376: GLU, Nonterminal, was not found in name map.) (Residue 377: LYS, Nonterminal, was not found in name map.) (Residue 378: PRO, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: ARG, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: HIS, Nonterminal, was not found in name map.) (Residue 383: PRO, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: HIS, Nonterminal, was not found in name map.) (Residue 386: PHE, Nonterminal, was not found in name map.) (Residue 387: LEU, Nonterminal, was not found in name map.) (Residue 388: ASP, Nonterminal, was not found in name map.) (Residue 389: ALA, Nonterminal, was not found in name map.) (Residue 390: GLN, Nonterminal, was not found in name map.) (Residue 391: GLY, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: PHE, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: LYS, Nonterminal, was not found in name map.) (Residue 396: PRO, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: ALA, Nonterminal, was not found in name map.) (Residue 399: PHE, Nonterminal, was not found in name map.) (Residue 400: LEU, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: PHE, Nonterminal, was not found in name map.) (Residue 403: SER, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: GLY, Nonterminal, was not found in name map.) (Residue 406: ARG, Nonterminal, was not found in name map.) (Residue 407: ARG, Nonterminal, was not found in name map.) (Residue 408: ALA, Nonterminal, was not found in name map.) (Residue 409: CYP, Nonterminal, was not found in name map.) (Residue 410: LEU, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLU, Nonterminal, was not found in name map.) (Residue 413: PRO, Nonterminal, was not found in name map.) (Residue 414: LEU, Nonterminal, was not found in name map.) (Residue 415: ALA, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: GLU, Nonterminal, was not found in name map.) (Residue 419: LEU, Nonterminal, was not found in name map.) (Residue 420: PHE, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: PHE, Nonterminal, was not found in name map.) (Residue 423: PHE, Nonterminal, was not found in name map.) (Residue 424: THR, Nonterminal, was not found in name map.) (Residue 425: SER, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: GLN, Nonterminal, was not found in name map.) (Residue 429: HIS, Nonterminal, was not found in name map.) (Residue 430: PHE, Nonterminal, was not found in name map.) (Residue 431: SER, Nonterminal, was not found in name map.) (Residue 432: PHE, Nonterminal, was not found in name map.) (Residue 433: SER, Nonterminal, was not found in name map.) (Residue 434: VAL, Nonterminal, was not found in name map.) (Residue 435: PRO, Nonterminal, was not found in name map.) (Residue 436: THR, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: GLN, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: ARG, Nonterminal, was not found in name map.) (Residue 441: PRO, Nonterminal, was not found in name map.) (Residue 442: SER, Nonterminal, was not found in name map.) (Residue 443: HIS, Nonterminal, was not found in name map.) (Residue 444: HIS, Nonterminal, was not found in name map.) (Residue 445: GLY, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: PHE, Nonterminal, was not found in name map.) (Residue 448: ALA, Nonterminal, was not found in name map.) (Residue 449: PHE, Nonterminal, was not found in name map.) (Residue 450: LEU, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: SER, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: SER, Nonterminal, was not found in name map.) (Residue 455: PRO, Nonterminal, was not found in name map.) (Residue 456: TYR, Nonterminal, was not found in name map.) (Residue 457: GLU, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: CYS, Nonterminal, was not found in name map.) (Residue 460: ALA, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: PRO, Nonterminal, was not found in name map.) Mapped residue ARG, term: Terminal/last, seq. number: 463 to: CARG. (Residue 464: HEM, Terminal/last, was not found in name map.) Joining NPRO - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TYR Joining TYR - CYS Joining CYS - PHE Joining PHE - ASP Joining ASP - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - SER Joining SER - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - THR Joining THR - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - VAL Joining VAL - THR Joining THR - HIE Joining HIE - GLY Joining GLY - GLU Joining GLU - ASP Joining ASP - THR Joining THR - ALA Joining ALA - ASP Joining ASP - ARG Joining ARG - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - THR Joining THR - GLN Joining GLN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - SER Joining SER - GLN Joining GLN - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ARG Joining ARG - GLU Joining GLU - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - THR Joining THR - LEU Joining LEU - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - GLY Joining GLY - LYS Joining LYS - LYS Joining LYS - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - HIE Joining HIE - SER Joining SER - GLY Joining GLY - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ILE Joining ILE - ALA Joining ALA - SER Joining SER - LEU Joining LEU - THR Joining THR - CYS Joining CYS - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - GLU Joining GLU - SER Joining SER - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - ASP Joining ASP - ARG Joining ARG - HIE Joining HIE - ILE Joining ILE - PRO Joining PRO - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - GLN Joining GLN - LYS Joining LYS - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - THR Joining THR - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - MET Joining MET - THR Joining THR - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - PRO Joining PRO - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - LEU Joining LEU - THR Joining THR - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLU Joining GLU - MET Joining MET - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - LYS Joining LYS - GLY Joining GLY - ASN Joining ASN - PRO Joining PRO - GLU Joining GLU - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - ASP Joining ASP - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - MET Joining MET - VAL Joining VAL - THR Joining THR - THR Joining THR - SER Joining SER - THR Joining THR - THR Joining THR - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - ARG Joining ARG - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - GLU Joining GLU - MET Joining MET - GLY Joining GLY - ASP Joining ASP - GLN Joining GLN - ALA Joining ALA - HIE Joining HIE - MET Joining MET - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HIE Joining HIE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - ARG Joining ARG - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - PRO Joining PRO - LEU Joining LEU - GLY Joining GLY - MET Joining MET - THR Joining THR - HIE Joining HIE - MET Joining MET - THR Joining THR - SER Joining SER - ARG Joining ARG - ASP Joining ASP - ILE Joining ILE - GLU Joining GLU - VAL Joining VAL - GLN Joining GLN - GLY Joining GLY - PHE Joining PHE - ARG Joining ARG - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - THR Joining THR - THR Joining THR - LEU Joining LEU - ILE Joining ILE - THR Joining THR - ASN Joining ASN - LEU Joining LEU - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - HIE Joining HIE - PHE Joining PHE - VAL Joining VAL - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - SER Joining SER - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - CYS Joining CYS - LEU Joining LEU - GLY Joining GLY - GLU Joining GLU - PRO Joining PRO - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - MET Joining MET - GLU Joining GLU - LEU Joining LEU - PHE Joining PHE - LEU Joining LEU - PHE Joining PHE - PHE Joining PHE - THR Joining THR - SER Joining SER - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - HIE Joining HIE - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - VAL Joining VAL - PRO Joining PRO - THR Joining THR - GLY Joining GLY - GLN Joining GLN - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - SER Joining SER - HIE Joining HIE - HIE Joining HIE - GLY Joining GLY - VAL Joining VAL - PHE Joining PHE - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - SER Joining SER - PRO Joining PRO - SER Joining SER - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - CYS Joining CYS - ALA Joining ALA - VAL Joining VAL - PRO Joining PRO - CARG total atoms in file: 3717 Leap added 3680 missing atoms according to residue templates: 3650 H / lone pairs 30 unknown element > bond aa.410.SG aa.465.FE > > saveamberparm aa m5_invacuo.topo m5_invacuo.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -6.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.397110 to meet diagonal cut criterion Solute vdw bounding box: 48.637 69.914 71.195 Total bounding box for atom centers: 104.725 104.725 104.725 (box expansion for 'iso' is 29.0%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 6 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 46.935873, 46.935873, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 46.935873, 46.935873, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 46.935873, 46.935873, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 46.935873, 46.935873, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 46.935873, 46.935873, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 46.935873, 46.935873, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 46.935873, 28.161524, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 46.935873, 28.161524, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 46.935873, 28.161524, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 46.935873, 28.161524, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 46.935873, 28.161524, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 46.935873, 28.161524, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 46.935873, 9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 46.935873, 9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 46.935873, 9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 46.935873, 9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 46.935873, 9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 46.935873, 9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 46.935873, -9.387175, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 46.935873, -9.387175, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 46.935873, -9.387175, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 46.935873, -9.387175, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 46.935873, -9.387175, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 46.935873, -9.387175, -46.935873 Adding box at: x=0 y=4 z=0 Center of solvent box is: 46.935873, -28.161524, 46.935873 Adding box at: x=0 y=4 z=1 Center of solvent box is: 46.935873, -28.161524, 28.161524 Adding box at: x=0 y=4 z=2 Center of solvent box is: 46.935873, -28.161524, 9.387175 Adding box at: x=0 y=4 z=3 Center of solvent box is: 46.935873, -28.161524, -9.387175 Adding box at: x=0 y=4 z=4 Center of solvent box is: 46.935873, -28.161524, -28.161524 Adding box at: x=0 y=4 z=5 Center of solvent box is: 46.935873, -28.161524, -46.935873 Adding box at: x=0 y=5 z=0 Center of solvent box is: 46.935873, -46.935873, 46.935873 Adding box at: x=0 y=5 z=1 Center of solvent box is: 46.935873, -46.935873, 28.161524 Adding box at: x=0 y=5 z=2 Center of solvent box is: 46.935873, -46.935873, 9.387175 Adding box at: x=0 y=5 z=3 Center of solvent box is: 46.935873, -46.935873, -9.387175 Adding box at: x=0 y=5 z=4 Center of solvent box is: 46.935873, -46.935873, -28.161524 Adding box at: x=0 y=5 z=5 Center of solvent box is: 46.935873, -46.935873, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 28.161524, 46.935873, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 28.161524, 46.935873, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 28.161524, 46.935873, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 28.161524, 46.935873, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 28.161524, 46.935873, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 28.161524, 46.935873, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 28.161524, 28.161524, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 28.161524, 28.161524, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 28.161524, 28.161524, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 28.161524, 28.161524, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 28.161524, 28.161524, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 28.161524, 28.161524, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 28.161524, 9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 28.161524, 9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 28.161524, 9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 28.161524, 9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 28.161524, 9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 28.161524, 9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 28.161524, -9.387175, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 28.161524, -9.387175, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 28.161524, -9.387175, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 28.161524, -9.387175, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 28.161524, -9.387175, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 28.161524, -9.387175, -46.935873 Adding box at: x=1 y=4 z=0 Center of solvent box is: 28.161524, -28.161524, 46.935873 Adding box at: x=1 y=4 z=1 Center of solvent box is: 28.161524, -28.161524, 28.161524 Adding box at: x=1 y=4 z=2 Center of solvent box is: 28.161524, -28.161524, 9.387175 Adding box at: x=1 y=4 z=3 Center of solvent box is: 28.161524, -28.161524, -9.387175 Adding box at: x=1 y=4 z=4 Center of solvent box is: 28.161524, -28.161524, -28.161524 Adding box at: x=1 y=4 z=5 Center of solvent box is: 28.161524, -28.161524, -46.935873 Adding box at: x=1 y=5 z=0 Center of solvent box is: 28.161524, -46.935873, 46.935873 Adding box at: x=1 y=5 z=1 Center of solvent box is: 28.161524, -46.935873, 28.161524 Adding box at: x=1 y=5 z=2 Center of solvent box is: 28.161524, -46.935873, 9.387175 Adding box at: x=1 y=5 z=3 Center of solvent box is: 28.161524, -46.935873, -9.387175 Adding box at: x=1 y=5 z=4 Center of solvent box is: 28.161524, -46.935873, -28.161524 Adding box at: x=1 y=5 z=5 Center of solvent box is: 28.161524, -46.935873, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 9.387175, 46.935873, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 9.387175, 46.935873, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 9.387175, 46.935873, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 9.387175, 46.935873, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 9.387175, 46.935873, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 9.387175, 46.935873, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 9.387175, 28.161524, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 9.387175, 28.161524, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 9.387175, 28.161524, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 9.387175, 28.161524, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 9.387175, 28.161524, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 9.387175, 28.161524, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 9.387175, 9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 9.387175, 9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 9.387175, 9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 9.387175, 9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 9.387175, -9.387175, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 9.387175, -9.387175, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 9.387175, -9.387175, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 9.387175, -9.387175, -46.935873 Adding box at: x=2 y=4 z=0 Center of solvent box is: 9.387175, -28.161524, 46.935873 Adding box at: x=2 y=4 z=1 Center of solvent box is: 9.387175, -28.161524, 28.161524 Adding box at: x=2 y=4 z=2 Center of solvent box is: 9.387175, -28.161524, 9.387175 Adding box at: x=2 y=4 z=3 Center of solvent box is: 9.387175, -28.161524, -9.387175 Adding box at: x=2 y=4 z=4 Center of solvent box is: 9.387175, -28.161524, -28.161524 Adding box at: x=2 y=4 z=5 Center of solvent box is: 9.387175, -28.161524, -46.935873 Adding box at: x=2 y=5 z=0 Center of solvent box is: 9.387175, -46.935873, 46.935873 Adding box at: x=2 y=5 z=1 Center of solvent box is: 9.387175, -46.935873, 28.161524 Adding box at: x=2 y=5 z=2 Center of solvent box is: 9.387175, -46.935873, 9.387175 Adding box at: x=2 y=5 z=3 Center of solvent box is: 9.387175, -46.935873, -9.387175 Adding box at: x=2 y=5 z=4 Center of solvent box is: 9.387175, -46.935873, -28.161524 Adding box at: x=2 y=5 z=5 Center of solvent box is: 9.387175, -46.935873, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -9.387175, 46.935873, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -9.387175, 46.935873, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -9.387175, 46.935873, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -9.387175, 46.935873, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -9.387175, 46.935873, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -9.387175, 46.935873, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -9.387175, 28.161524, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -9.387175, 28.161524, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -9.387175, 28.161524, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -9.387175, 28.161524, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -9.387175, 28.161524, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -9.387175, 28.161524, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -9.387175, 9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -9.387175, 9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -9.387175, 9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -9.387175, 9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -9.387175, -9.387175, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -9.387175, -9.387175, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -9.387175, -9.387175, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -9.387175, -9.387175, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -9.387175, -9.387175, -46.935873 Adding box at: x=3 y=4 z=0 Center of solvent box is: -9.387175, -28.161524, 46.935873 Adding box at: x=3 y=4 z=1 Center of solvent box is: -9.387175, -28.161524, 28.161524 Adding box at: x=3 y=4 z=2 Center of solvent box is: -9.387175, -28.161524, 9.387175 Adding box at: x=3 y=4 z=3 Center of solvent box is: -9.387175, -28.161524, -9.387175 Adding box at: x=3 y=4 z=4 Center of solvent box is: -9.387175, -28.161524, -28.161524 Adding box at: x=3 y=4 z=5 Center of solvent box is: -9.387175, -28.161524, -46.935873 Adding box at: x=3 y=5 z=0 Center of solvent box is: -9.387175, -46.935873, 46.935873 Adding box at: x=3 y=5 z=1 Center of solvent box is: -9.387175, -46.935873, 28.161524 Adding box at: x=3 y=5 z=2 Center of solvent box is: -9.387175, -46.935873, 9.387175 Adding box at: x=3 y=5 z=3 Center of solvent box is: -9.387175, -46.935873, -9.387175 Adding box at: x=3 y=5 z=4 Center of solvent box is: -9.387175, -46.935873, -28.161524 Adding box at: x=3 y=5 z=5 Center of solvent box is: -9.387175, -46.935873, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -28.161524, 46.935873, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -28.161524, 46.935873, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -28.161524, 46.935873, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -28.161524, 46.935873, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -28.161524, 46.935873, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -28.161524, 46.935873, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -28.161524, 28.161524, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -28.161524, 28.161524, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -28.161524, 28.161524, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -28.161524, 28.161524, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -28.161524, 28.161524, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -28.161524, 28.161524, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -28.161524, 9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -28.161524, 9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -28.161524, 9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -28.161524, 9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -28.161524, 9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -28.161524, 9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -28.161524, -9.387175, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -28.161524, -9.387175, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -28.161524, -9.387175, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -28.161524, -9.387175, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -28.161524, -9.387175, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -28.161524, -9.387175, -46.935873 Adding box at: x=4 y=4 z=0 Center of solvent box is: -28.161524, -28.161524, 46.935873 Adding box at: x=4 y=4 z=1 Center of solvent box is: -28.161524, -28.161524, 28.161524 Adding box at: x=4 y=4 z=2 Center of solvent box is: -28.161524, -28.161524, 9.387175 Adding box at: x=4 y=4 z=3 Center of solvent box is: -28.161524, -28.161524, -9.387175 Adding box at: x=4 y=4 z=4 Center of solvent box is: -28.161524, -28.161524, -28.161524 Adding box at: x=4 y=4 z=5 Center of solvent box is: -28.161524, -28.161524, -46.935873 Adding box at: x=4 y=5 z=0 Center of solvent box is: -28.161524, -46.935873, 46.935873 Adding box at: x=4 y=5 z=1 Center of solvent box is: -28.161524, -46.935873, 28.161524 Adding box at: x=4 y=5 z=2 Center of solvent box is: -28.161524, -46.935873, 9.387175 Adding box at: x=4 y=5 z=3 Center of solvent box is: -28.161524, -46.935873, -9.387175 Adding box at: x=4 y=5 z=4 Center of solvent box is: -28.161524, -46.935873, -28.161524 Adding box at: x=4 y=5 z=5 Center of solvent box is: -28.161524, -46.935873, -46.935873 Adding box at: x=5 y=0 z=0 Center of solvent box is: -46.935873, 46.935873, 46.935873 Adding box at: x=5 y=0 z=1 Center of solvent box is: -46.935873, 46.935873, 28.161524 Adding box at: x=5 y=0 z=2 Center of solvent box is: -46.935873, 46.935873, 9.387175 Adding box at: x=5 y=0 z=3 Center of solvent box is: -46.935873, 46.935873, -9.387175 Adding box at: x=5 y=0 z=4 Center of solvent box is: -46.935873, 46.935873, -28.161524 Adding box at: x=5 y=0 z=5 Center of solvent box is: -46.935873, 46.935873, -46.935873 Adding box at: x=5 y=1 z=0 Center of solvent box is: -46.935873, 28.161524, 46.935873 Adding box at: x=5 y=1 z=1 Center of solvent box is: -46.935873, 28.161524, 28.161524 Adding box at: x=5 y=1 z=2 Center of solvent box is: -46.935873, 28.161524, 9.387175 Adding box at: x=5 y=1 z=3 Center of solvent box is: -46.935873, 28.161524, -9.387175 Adding box at: x=5 y=1 z=4 Center of solvent box is: -46.935873, 28.161524, -28.161524 Adding box at: x=5 y=1 z=5 Center of solvent box is: -46.935873, 28.161524, -46.935873 Adding box at: x=5 y=2 z=0 Center of solvent box is: -46.935873, 9.387175, 46.935873 Adding box at: x=5 y=2 z=1 Center of solvent box is: -46.935873, 9.387175, 28.161524 Adding box at: x=5 y=2 z=2 Center of solvent box is: -46.935873, 9.387175, 9.387175 Adding box at: x=5 y=2 z=3 Center of solvent box is: -46.935873, 9.387175, -9.387175 Adding box at: x=5 y=2 z=4 Center of solvent box is: -46.935873, 9.387175, -28.161524 Adding box at: x=5 y=2 z=5 Center of solvent box is: -46.935873, 9.387175, -46.935873 Adding box at: x=5 y=3 z=0 Center of solvent box is: -46.935873, -9.387175, 46.935873 Adding box at: x=5 y=3 z=1 Center of solvent box is: -46.935873, -9.387175, 28.161524 Adding box at: x=5 y=3 z=2 Center of solvent box is: -46.935873, -9.387175, 9.387175 Adding box at: x=5 y=3 z=3 Center of solvent box is: -46.935873, -9.387175, -9.387175 Adding box at: x=5 y=3 z=4 Center of solvent box is: -46.935873, -9.387175, -28.161524 Adding box at: x=5 y=3 z=5 Center of solvent box is: -46.935873, -9.387175, -46.935873 Adding box at: x=5 y=4 z=0 Center of solvent box is: -46.935873, -28.161524, 46.935873 Adding box at: x=5 y=4 z=1 Center of solvent box is: -46.935873, -28.161524, 28.161524 Adding box at: x=5 y=4 z=2 Center of solvent box is: -46.935873, -28.161524, 9.387175 Adding box at: x=5 y=4 z=3 Center of solvent box is: -46.935873, -28.161524, -9.387175 Adding box at: x=5 y=4 z=4 Center of solvent box is: -46.935873, -28.161524, -28.161524 Adding box at: x=5 y=4 z=5 Center of solvent box is: -46.935873, -28.161524, -46.935873 Adding box at: x=5 y=5 z=0 Center of solvent box is: -46.935873, -46.935873, 46.935873 Adding box at: x=5 y=5 z=1 Center of solvent box is: -46.935873, -46.935873, 28.161524 Adding box at: x=5 y=5 z=2 Center of solvent box is: -46.935873, -46.935873, 9.387175 Adding box at: x=5 y=5 z=3 Center of solvent box is: -46.935873, -46.935873, -9.387175 Adding box at: x=5 y=5 z=4 Center of solvent box is: -46.935873, -46.935873, -28.161524 Adding box at: x=5 y=5 z=5 Center of solvent box is: -46.935873, -46.935873, -46.935873 Volume: 590891.441 A^3 (oct) Total mass 320266.290 amu, Density 0.900 g/cc Added 14855 residues. > > addions aa Na+ 0 6 Na+ ions required to neutralize. Adding 6 counter ions to "aa" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -34.08 -42.23 -39.36 41.69 39.47 37.00 sized: 93.92 85.77 88.64 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.15% of box, grid points 87134 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 83 sec (Replacing solvent molecule) Placed Na+ in aa at (30.10, 0.21, 5.87). (Replacing solvent molecule) Placed Na+ in aa at (-0.15, -38.07, -3.98). (No solvent overlap) Placed Na+ in aa at (23.78, -15.31, -10.45). (No solvent overlap) Placed Na+ in aa at (25.78, 11.69, 10.55). (Replacing solvent molecule) Placed Na+ in aa at (-27.83, -4.32, -1.56). (Replacing solvent molecule) Placed Na+ in aa at (22.17, -4.97, -20.32). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -35.15 -45.39 -38.45 41.97 38.17 37.55 sized: 92.85 82.61 89.55 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.12% of box, grid points 86385 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 89 sec (No solvent overlap) Placed Na+ in aa at (-4.22, -36.51, -1.67). (No solvent overlap) Placed Na+ in aa at (-3.22, 13.49, 21.33). (Replacing solvent molecule) Placed Na+ in aa at (-23.89, -12.81, -3.63). (Replacing solvent molecule) Placed Na+ in aa at (24.83, -17.06, -16.86). (No solvent overlap) Placed Na+ in aa at (18.78, -26.51, 3.33). (Replacing solvent molecule) Placed Na+ in aa at (-20.67, 1.63, 23.77). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.22 -43.83 -43.67 43.83 38.27 37.09 sized: 95.78 84.17 84.33 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.26% of box, grid points 89271 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 105 sec (No solvent overlap) Placed Na+ in aa at (-13.49, 7.52, -10.95). (Replacing solvent molecule) Placed Cl- in aa at (12.59, 4.91, 20.68). (Replacing solvent molecule) Placed Na+ in aa at (13.16, 10.29, 22.81). (Replacing solvent molecule) Placed Cl- in aa at (17.48, 12.65, 21.07). (Replacing solvent molecule) Placed Na+ in aa at (17.69, 16.82, 22.88). (Replacing solvent molecule) Placed Cl- in aa at (14.27, 15.85, 25.72). (Replacing solvent molecule) Placed Na+ in aa at (20.21, 13.69, 21.24). (Replacing solvent molecule) Placed Cl- in aa at (18.88, 18.00, 19.38). (Replacing solvent molecule) Placed Na+ in aa at (10.69, 6.28, 24.19). (Replacing solvent molecule) Placed Cl- in aa at (9.23, 10.85, 22.81). (Replacing solvent molecule) Placed Na+ in aa at (6.78, -32.06, -1.24). (Replacing solvent molecule) Placed Cl- in aa at (34.99, 11.19, -3.74). (Replacing solvent molecule) Placed Na+ in aa at (36.99, 10.62, -0.01). (Replacing solvent molecule) Placed Cl- in aa at (19.31, -15.30, -20.55). (Replacing solvent molecule) Placed Na+ in aa at (37.29, 11.73, -5.29). (Replacing solvent molecule) Placed Cl- in aa at (37.70, 16.08, -2.79). (Replacing solvent molecule) Placed Na+ in aa at (9.42, 13.59, 23.46). (Replacing solvent molecule) Placed Cl- in aa at (38.04, 10.46, -2.87). (Replacing solvent molecule) Placed Na+ in aa at (22.32, -12.37, -18.27). (Replacing solvent molecule) Placed Cl- in aa at (24.27, -7.09, -20.35). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.96 -43.95 -38.42 45.83 40.01 38.10 sized: 94.04 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 4.71% of box, grid points 98754 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 120 sec (Replacing solvent molecule) Placed Na+ in aa at (-5.35, -36.65, -2.92). (Replacing solvent molecule) Placed Na+ in aa at (19.26, -24.63, 2.72). (Replacing solvent molecule) Placed Na+ in aa at (-2.75, 18.44, 19.78). (No solvent overlap) Placed Na+ in aa at (-24.92, -9.12, -4.26). (Replacing solvent molecule) Placed Na+ in aa at (19.38, -20.58, -6.20). (Replacing solvent molecule) Placed Na+ in aa at (-13.32, 8.44, -13.97). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -32.92 -43.97 -38.26 43.51 39.59 37.38 sized: 95.08 84.03 89.74 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.08% of box, grid points 85522 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 98 sec (Replacing solvent molecule) Placed Na+ in aa at (-14.28, -34.58, -13.38). (Replacing solvent molecule) Placed Cl- in aa at (31.86, 16.78, -7.41). (Replacing solvent molecule) Placed Na+ in aa at (30.28, 18.17, -3.60). (Replacing solvent molecule) Placed Cl- in aa at (30.77, 22.08, -2.41). (Replacing solvent molecule) Placed Na+ in aa at (30.10, 23.21, -7.41). (Replacing solvent molecule) Placed Cl- in aa at (-16.07, 24.24, -6.06). (Replacing solvent molecule) Placed Na+ in aa at (30.49, 18.49, 0.70). (Replacing solvent molecule) Placed Cl- in aa at (28.96, 19.04, 3.16). (Replacing solvent molecule) Placed Na+ in aa at (26.10, 24.36, 2.67). (Replacing solvent molecule) Placed Cl- in aa at (34.93, 18.51, 1.29). (Replacing solvent molecule) Placed Na+ in aa at (26.40, 19.58, 7.85). (Replacing solvent molecule) Placed Cl- in aa at (26.35, 24.18, 6.21). (Replacing solvent molecule) Placed Na+ in aa at (-16.21, 25.98, -3.01). (Replacing solvent molecule) Placed Cl- in aa at (-17.15, 18.25, 4.77). (Replacing solvent molecule) Placed Na+ in aa at (-21.41, 15.15, 5.83). (Replacing solvent molecule) Placed Cl- in aa at (-13.36, 24.66, 0.17). (Replacing solvent molecule) Placed Na+ in aa at (-14.96, 17.68, 7.28). (Replacing solvent molecule) Placed Cl- in aa at (14.14, 22.02, 8.04). (Replacing solvent molecule) Placed Na+ in aa at (14.94, 19.22, 11.83). (Replacing solvent molecule) Placed Cl- in aa at (17.98, 21.80, 9.18). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -45.86 -38.92 42.72 38.64 38.02 sized: 92.38 82.14 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.70% of box, grid points 98597 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 160 sec (Replacing solvent molecule) Placed Na+ in aa at (-7.43, 14.17, 21.20). (Replacing solvent molecule) Placed Na+ in aa at (-3.21, -36.76, -1.30). (Replacing solvent molecule) Placed Na+ in aa at (-17.04, 7.27, -12.93). (Replacing solvent molecule) Placed Na+ in aa at (-26.32, -12.13, -4.77). (Replacing solvent molecule) Placed Na+ in aa at (19.44, -20.57, -6.46). (No solvent overlap) Placed Na+ in aa at (-13.08, 2.77, 28.64). Done adding ions. > > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.32 to 7.32 Box: enclosing: -34.08 -44.08 -39.36 41.69 39.47 37.00 sized: 93.92 83.92 88.64 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.18% of box, grid points 87729 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 95 sec (Replacing solvent molecule) Placed Na+ in aa at (-24.61, 6.83, 5.29). (Replacing solvent molecule) Placed Cl- in aa at (-24.43, 10.78, 6.51). (Replacing solvent molecule) Placed Na+ in aa at (-21.94, 12.43, 4.64). (Replacing solvent molecule) Placed Cl- in aa at (-23.85, 11.99, 2.59). (Replacing solvent molecule) Placed Na+ in aa at (-25.44, 15.68, 8.25). (Replacing solvent molecule) Placed Cl- in aa at (-22.35, 15.65, 8.87). (Replacing solvent molecule) Placed Na+ in aa at (-26.38, 10.86, 8.77). (Replacing solvent molecule) Placed Cl- in aa at (-19.09, 16.52, 2.29). (Replacing solvent molecule) Placed Na+ in aa at (-23.74, 16.26, 2.04). (Replacing solvent molecule) Placed Cl- in aa at (13.03, 6.36, 27.20). (Replacing solvent molecule) Placed Na+ in aa at (15.31, 8.85, 29.36). (Replacing solvent molecule) Placed Cl- in aa at (-29.57, 6.95, 17.97). (Replacing solvent molecule) Placed Na+ in aa at (-26.86, 8.72, 20.63). (Replacing solvent molecule) Placed Cl- in aa at (-27.58, 7.70, 9.91). (Replacing solvent molecule) Placed Na+ in aa at (-28.51, 6.39, 12.40). (Replacing solvent molecule) Placed Cl- in aa at (-27.00, 10.46, 23.68). (Replacing solvent molecule) Placed Na+ in aa at (-30.86, 3.94, 19.79). (Replacing solvent molecule) Placed Cl- in aa at (-27.29, 2.54, 16.09). (Replacing solvent molecule) Placed Na+ in aa at (-30.14, 11.50, 19.58). (Replacing solvent molecule) Placed Cl- in aa at (-27.64, 11.64, 18.39). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -38.65 -43.95 -38.42 45.83 40.01 38.10 sized: 89.35 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 4.89% of box, grid points 102560 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 156 sec (Replacing solvent molecule) Placed Na+ in aa at (-12.93, 8.47, -11.40). (Replacing solvent molecule) Placed Cl- in aa at (-17.12, 7.13, -12.84). (Replacing solvent molecule) Placed Na+ in aa at (-18.60, 4.20, -10.50). (Replacing solvent molecule) Placed Cl- in aa at (13.41, 0.45, 19.31). (Replacing solvent molecule) Placed Na+ in aa at (16.28, 0.98, 19.40). (Replacing solvent molecule) Placed Cl- in aa at (23.87, -18.37, -19.22). (Replacing solvent molecule) Placed Na+ in aa at (29.01, -20.43, -16.88). (Replacing solvent molecule) Placed Cl- in aa at (27.30, -16.78, -14.27). (Replacing solvent molecule) Placed Na+ in aa at (28.67, -16.25, -11.97). (Replacing solvent molecule) Placed Cl- in aa at (31.63, -17.13, -19.21). (Replacing solvent molecule) Placed Na+ in aa at (27.09, -16.58, -18.41). (Replacing solvent molecule) Placed Cl- in aa at (34.96, 11.06, -3.91). (Replacing solvent molecule) Placed Na+ in aa at (38.15, 8.59, -6.09). (Replacing solvent molecule) Placed Cl- in aa at (15.41, 5.52, 21.37). (Replacing solvent molecule) Placed Na+ in aa at (10.67, 6.15, 24.02). (Replacing solvent molecule) Placed Cl- in aa at (9.20, 10.73, 22.64). (Replacing solvent molecule) Placed Na+ in aa at (12.72, 12.92, 22.63). (Replacing solvent molecule) Placed Cl- in aa at (14.34, 12.19, 20.19). (Replacing solvent molecule) Placed Na+ in aa at (18.00, 9.59, 17.80). (Replacing solvent molecule) Placed Cl- in aa at (20.43, 11.87, 19.02). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -32.69 -44.30 -44.14 45.94 38.74 37.56 sized: 95.31 83.70 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.82% of box, grid points 101143 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 166 sec (Replacing solvent molecule) Placed Na+ in aa at (-18.38, 1.22, 29.44). (Replacing solvent molecule) Placed Cl- in aa at (12.60, 1.91, 16.03). (No solvent overlap) Placed Na+ in aa at (11.08, 3.03, 12.74). (Replacing solvent molecule) Placed Cl- in aa at (-9.76, 7.06, -14.91). (Replacing solvent molecule) Placed Na+ in aa at (-14.13, 3.57, -14.50). (Replacing solvent molecule) Placed Cl- in aa at (-13.62, -0.66, -14.69). (No solvent overlap) Placed Na+ in aa at (-13.92, 2.03, -9.26). (Replacing solvent molecule) Placed Cl- in aa at (-14.90, 6.27, -14.51). (Replacing solvent molecule) Placed Na+ in aa at (-11.48, 8.98, -15.90). (Replacing solvent molecule) Placed Cl- in aa at (-14.32, 13.28, -16.62). (Replacing solvent molecule) Placed Na+ in aa at (-14.11, 16.89, -14.31). (Replacing solvent molecule) Placed Cl- in aa at (-10.94, 19.04, -12.30). (Replacing solvent molecule) Placed Na+ in aa at (-10.56, 24.38, -12.66). (Replacing solvent molecule) Placed Cl- in aa at (-10.57, 27.43, -10.32). charges: 137 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.71, 31.06, -6.50). (Replacing solvent molecule) Placed Na+ in aa at (23.85, -26.26, -1.53). (Replacing solvent molecule) Placed Cl- in aa at (-8.58, 33.16, -3.03). (Replacing solvent molecule) Placed Cl- in aa at (26.22, -24.82, -5.15). (Replacing solvent molecule) Placed Na+ in aa at (-6.84, 31.46, -4.04). (Replacing solvent molecule) Placed Na+ in aa at (24.73, -26.14, -10.47). (Replacing solvent molecule) Placed Cl- in aa at (-6.35, 33.91, -6.28). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (26.04, -27.76, -2.04). Placed Na+ in aa at (-5.61, 33.20, -10.46). (Replacing solvent molecule) Placed Cl- in aa at (-6.11, 25.21, -13.67). Done adding ions. > addions aa Na+ 10 Cl- 10 (Replacing solvent molecule) Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 41.70 37.85 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Placed Na+ in aa at (23.95, -20.18, -3.88). grid build: 2 sec Volume = 4.59% of box, grid points 96244 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Cl- in aa at (20.57, -23.76, -9.80). (Replacing solvent molecule) Placed Na+ in aa at (27.77, -27.28, -4.64). (Replacing solvent molecule) Placed Cl- in aa at (14.05, 14.81, 13.62). (No solvent overlap) Placed Na+ in aa at (15.38, 15.14, 10.08). (Replacing solvent molecule) Placed Cl- in aa at (23.66, -28.22, -14.48). (Replacing solvent molecule) Placed Na+ in aa at (16.01, -27.93, -10.60). (Replacing solvent molecule) Placed Cl- in aa at (16.43, -31.79, -14.24). (Replacing solvent molecule) Placed Na+ in aa at (18.36, -28.91, -14.45). (Replacing solvent molecule) Placed Cl- in aa at (14.13, -29.13, -8.95). (Replacing solvent molecule) Placed Na+ in aa at (9.37, -32.21, -3.22). (Replacing solvent molecule) Placed Cl- in aa at (9.73, -16.09, -23.08). (Replacing solvent molecule) Placed Na+ in aa at (4.23, -37.12, 1.64). (Replacing solvent molecule) Placed Cl- in aa at (7.50, -34.57, -1.36). (Replacing solvent molecule) Placed Na+ in aa at (17.98, -36.08, -8.72). (Replacing solvent molecule) Placed Cl- in aa at (10.89, -33.95, -7.57). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -45.86 -38.92 42.72 38.64 38.02 sized: 92.38 82.14 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.80% of box, grid points 100653 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 136 sec (Replacing solvent molecule) Placed Na+ in aa at (-15.80, -30.06, -7.08). (Replacing solvent molecule) Placed Cl- in aa at (11.44, 2.52, 19.38). (Replacing solvent molecule) Placed Na+ in aa at (9.40, 1.41, 16.98). (Replacing solvent molecule) Placed Cl- in aa at (10.07, -1.47, 14.13). (Replacing solvent molecule) Placed Na+ in aa at (8.84, -6.72, 15.05). (Replacing solvent molecule) Placed Cl- in aa at (6.20, -12.13, 21.79). (Replacing solvent molecule) Placed Na+ in aa at (5.00, -15.29, 22.92). (Replacing solvent molecule) Placed Cl- in aa at (8.73, -11.00, 15.60). (Replacing solvent molecule) Placed Na+ in aa at (10.29, -14.06, 19.02). (Replacing solvent molecule) Placed Cl- in aa at (7.97, -16.16, 18.31). (Replacing solvent molecule) Placed Na+ in aa at (10.22, -17.11, 7.89). (Replacing solvent molecule) Placed Cl- in aa at (12.93, -13.09, 6.58). (Replacing solvent molecule) Placed Na+ in aa at (16.72, -7.07, 6.20). (Replacing solvent molecule) Placed Cl- in aa at (8.95, -19.82, 8.57). (Replacing solvent molecule) Placed Na+ in aa at (8.43, -13.85, 13.32). (Replacing solvent molecule) Placed Cl- in aa at (6.84, -9.06, 11.78). (Replacing solvent molecule) Placed Na+ in aa at (5.58, -12.53, 10.14). (Replacing solvent molecule) Placed Cl- in aa at (5.89, -15.53, 9.84). (Replacing solvent molecule) Placed Na+ in aa at (4.87, -17.86, 8.66). (Replacing solvent molecule) Placed Cl- in aa at (3.41, -16.49, 21.20). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.55 -44.55 -39.83 42.16 39.94 37.47 sized: 93.45 83.45 88.17 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.66% of box, grid points 97708 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 124 sec (Replacing solvent molecule) Placed Na+ in aa at (20.97, -24.91, -5.29). (Replacing solvent molecule) Placed Cl- in aa at (26.38, -20.90, -13.84). (Replacing solvent molecule) Placed Na+ in aa at (26.84, -22.38, -16.23). (Replacing solvent molecule) Placed Cl- in aa at (28.58, -22.04, -21.75). (Replacing solvent molecule) Placed Na+ in aa at (27.51, -18.96, -20.17). (Replacing solvent molecule) Placed Cl- in aa at (31.08, -24.86, -16.53). (Replacing solvent molecule) Placed Na+ in aa at (31.85, -21.81, -16.07). (Replacing solvent molecule) Placed Cl- in aa at (31.39, -19.36, -14.83). (Replacing solvent molecule) Placed Na+ in aa at (34.29, -18.03, -17.44). (Replacing solvent molecule) Placed Cl- in aa at (28.48, -15.46, -23.06). (Replacing solvent molecule) Placed Na+ in aa at (28.43, -13.30, -19.30). (Replacing solvent molecule) Placed Cl- in aa at (31.29, -12.14, -15.42). (Replacing solvent molecule) Placed Na+ in aa at (29.57, -10.12, -14.91). (Replacing solvent molecule) Placed Cl- in aa at (29.35, -10.76, -19.60). (Replacing solvent molecule) Placed Na+ in aa at (29.56, -8.63, -21.42). (Replacing solvent molecule) Placed Cl- in aa at (31.58, -8.05, -14.78). charges: 146 sec (Replacing solvent molecule) (Replacing solvent molecule) Placed Na+ in aa at (-24.92, 1.83, 14.97). Placed Na+ in aa at (33.03, -12.95, -7.07). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (-27.27, 15.07, 4.87). Placed Cl- in aa at (31.27, -18.79, -7.53). (Replacing solvent molecule) Placed Na+ in aa at (-30.49, 17.56, 6.84). (Replacing solvent molecule) Placed Na+ in aa at (33.56, -19.73, -11.09). (Replacing solvent molecule) Placed Cl- in aa at (-28.26, 15.75, 9.60). (Replacing solvent molecule) Placed Cl- in aa at (35.92, -22.60, -14.27). (Replacing solvent molecule) Placed Na+ in aa at (-30.77, 12.57, 7.40). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -32.69 -44.30 -44.14 45.94 38.74 37.56 sized: 95.31 83.70 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 (Replacing solvent molecule) Placed Cl- in aa at (-32.66, 13.95, 10.91). (Replacing solvent molecule) Placed Na+ in aa at (-29.41, 11.99, 2.94). (Replacing solvent molecule) Placed Cl- in aa at (-33.58, 14.38, 3.61). (Replacing solvent molecule) Placed Na+ in aa at (-30.33, 14.02, 13.93). (Replacing solvent molecule) Placed Cl- in aa at (-29.92, 8.24, 6.20). (Replacing solvent molecule) Placed Na+ in aa at (-27.96, 5.18, 5.89). (Replacing solvent molecule) Placed Cl- in aa at (-25.75, 2.16, 7.42). (Replacing solvent molecule) Placed Na+ in aa at (-28.37, 3.70, 11.97). (Replacing solvent molecule) Placed Cl- in aa at (-31.01, 5.12, 14.00). grid build: 2 sec Volume = 4.93% of box, grid points 103484 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in aa at (-35.42, 4.76, 13.48). (Replacing solvent molecule) Placed Cl- in aa at (-31.88, 2.96, 8.28). (Replacing solvent molecule) Placed Na+ in aa at (-33.47, 5.12, 10.44). (Replacing solvent molecule) Placed Cl- in aa at (-36.00, 9.20, 12.45). (Replacing solvent molecule) Placed Na+ in aa at (-34.00, 8.37, 16.32). (Replacing solvent molecule) Placed Cl- in aa at (-35.12, 3.07, 16.87). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -43.79 -43.95 -38.42 45.83 40.01 38.10 sized: 84.21 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.99% of box, grid points 104575 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 151 sec (Replacing solvent molecule) Placed Na+ in aa at (-18.34, -29.32, -8.82). (Replacing solvent molecule) Placed Cl- in aa at (20.48, 18.65, 11.30). (Replacing solvent molecule) Placed Na+ in aa at (17.25, 20.21, 14.18). (Replacing solvent molecule) Placed Cl- in aa at (14.21, 17.44, 14.04). (Replacing solvent molecule) Placed Na+ in aa at (16.48, 14.00, 12.45). (Replacing solvent molecule) Placed Cl- in aa at (18.03, 14.80, 17.79). (Replacing solvent molecule) Placed Na+ in aa at (21.68, 14.32, 17.17). (Replacing solvent molecule) Placed Cl- in aa at (16.33, 17.00, 10.35). (Replacing solvent molecule) Placed Na+ in aa at (15.31, 25.95, -0.01). (Replacing solvent molecule) Placed Cl- in aa at (12.60, 24.90, 2.75). (Replacing solvent molecule) Placed Na+ in aa at (10.00, 32.21, 4.79). (Replacing solvent molecule) Placed Cl- in aa at (11.11, 35.09, 2.96). (Replacing solvent molecule) Placed Na+ in aa at (18.03, 21.61, 9.31). (Replacing solvent molecule) Placed Cl- in aa at (8.32, 37.21, 7.14). (Replacing solvent molecule) Placed Na+ in aa at (6.93, 39.40, 4.97). (Replacing solvent molecule) Placed Cl- in aa at (12.59, 27.90, 7.40). (Replacing solvent molecule) Placed Na+ in aa at (4.77, 34.72, 7.98). (Replacing solvent molecule) Placed Cl- in aa at (1.98, 37.15, 5.79). (No solvent overlap) Placed Na+ in aa at (2.61, 31.56, 4.27). (Replacing solvent molecule) Placed Cl- in aa at (3.06, 30.93, 8.48). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 47.19 37.85 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.71% of box, grid points 98746 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 148 sec (Replacing solvent molecule) Placed Na+ in aa at (22.61, -13.80, -15.68). (Replacing solvent molecule) Placed Cl- in aa at (22.00, -15.98, -23.85). (Replacing solvent molecule) Placed Na+ in aa at (18.09, -13.27, -22.12). (Replacing solvent molecule) Placed Cl- in aa at (21.60, -18.26, -16.75). (Replacing solvent molecule) Placed Na+ in aa at (23.96, -18.24, -19.32). (Replacing solvent molecule) Placed Cl- in aa at (24.37, -13.87, -20.33). (Replacing solvent molecule) Placed Na+ in aa at (22.94, -11.77, -21.66). (Replacing solvent molecule) Placed Cl- in aa at (14.23, -12.28, -22.85). (Replacing solvent molecule) Placed Na+ in aa at (11.17, -10.89, -23.85). (Replacing solvent molecule) Placed Cl- in aa at (10.44, -7.86, -26.58). (No solvent overlap) Placed Na+ in aa at (8.45, -11.55, -26.83). (Replacing solvent molecule) Placed Cl- in aa at (11.18, -13.93, -26.20). (Replacing solvent molecule) Placed Na+ in aa at (-26.99, 8.78, 6.04). (Replacing solvent molecule) Placed Cl- in aa at (-27.90, 5.19, 5.63). (Replacing solvent molecule) Placed Na+ in aa at (-31.26, 3.56, 4.89). (Replacing solvent molecule) Placed Cl- in aa at (-29.07, 3.95, -1.10). (Replacing solvent molecule) Placed Na+ in aa at (-29.87, 1.20, 2.03). (Replacing solvent molecule) Placed Cl- in aa at (10.17, -10.49, -32.74). (Replacing solvent molecule) Placed Na+ in aa at (14.07, -9.26, -30.23). (Replacing solvent molecule) Placed Cl- in aa at (-28.92, -1.56, 5.32). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.05 -44.55 -40.53 42.16 39.94 37.47 sized: 88.95 83.45 87.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.80% of box, grid points 100626 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 192 sec (No solvent overlap) Placed Na+ in aa at (22.38, 8.14, 13.08). (Replacing solvent molecule) Placed Cl- in aa at (22.83, 11.40, 18.29). (Replacing solvent molecule) Placed Na+ in aa at (20.16, 13.88, 21.10). (Replacing solvent molecule) Placed Cl- in aa at (18.83, 18.19, 19.25). (Replacing solvent molecule) Placed Na+ in aa at (21.63, 14.51, 17.03). (Replacing solvent molecule) Placed Cl- in aa at (17.43, 12.84, 20.93). (Replacing solvent molecule) Placed Na+ in aa at (14.78, 13.94, 16.05). (Replacing solvent molecule) Placed Cl- in aa at (27.20, 5.84, 12.46). (Replacing solvent molecule) Placed Na+ in aa at (12.70, 13.24, 22.66). (Replacing solvent molecule) Placed Cl- in aa at (12.92, 15.92, 19.91). (Replacing solvent molecule) Placed Na+ in aa at (9.81, 18.70, 21.72). (Replacing solvent molecule) Placed Cl- in aa at (9.18, 11.04, 22.67). (Replacing solvent molecule) Placed Na+ in aa at (26.20, 3.62, 17.47). (Replacing solvent molecule) Placed Cl- in aa at (20.72, 22.92, 11.80). (Replacing solvent molecule) Placed Na+ in aa at (24.07, 24.11, 9.56). (Replacing solvent molecule) Placed Cl- in aa at (11.66, 17.04, 10.99). (Replacing solvent molecule) Placed Na+ in aa at (24.11, 20.79, 12.57). (Replacing solvent molecule) Placed Cl- in aa at (28.41, 21.78, 11.90). (Replacing solvent molecule) Placed Na+ in aa at (10.71, 19.48, 17.58). (Replacing solvent molecule) Placed Cl- in aa at (9.93, 21.51, 20.65). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -45.86 -38.92 42.72 38.64 38.02 sized: 92.38 82.14 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.89% of box, grid points 102565 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 197 sec (No solvent overlap) Placed Na+ in aa at (-14.69, -31.30, -11.14). (Replacing solvent molecule) Placed Cl- in aa at (-19.57, -30.39, -6.67). (Replacing solvent molecule) Placed Na+ in aa at (-12.09, -34.12, -7.53). (Replacing solvent molecule) Placed Cl- in aa at (9.39, 3.12, 26.60). (Replacing solvent molecule) Placed Na+ in aa at (9.99, 3.47, 29.67). (Replacing solvent molecule) Placed Cl- in aa at (-14.51, -36.39, -8.75). (Replacing solvent molecule) Placed Na+ in aa at (-16.98, -36.23, -13.84). (Replacing solvent molecule) Placed Cl- in aa at (-18.44, -31.50, -12.96). (Replacing solvent molecule) Placed Na+ in aa at (-20.26, -28.21, -10.95). (Replacing solvent molecule) Placed Cl- in aa at (-24.93, -24.00, -6.89). (Replacing solvent molecule) Placed Na+ in aa at (-21.38, -23.55, -8.24). (Replacing solvent molecule) Placed Cl- in aa at (-23.56, -23.50, -13.28). (Replacing solvent molecule) Placed Na+ in aa at (-27.10, -21.51, -12.15). (Replacing solvent molecule) Placed Cl- in aa at (22.85, -24.63, -16.37). charges: 122 sec (No solvent overlap) Placed Na+ in aa at (-11.39, 15.56, 12.27). (Replacing solvent molecule) Placed Na+ in aa at (20.45, -27.47, -15.42). (Replacing solvent molecule) Placed Cl- in aa at (14.85, 21.72, 12.40). (Replacing solvent molecule) Placed Cl- in aa at (16.30, -29.12, -16.37). (Replacing solvent molecule) Placed Na+ in aa at (19.20, 22.94, 14.73). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (22.16, 19.64, 17.06). Placed Na+ in aa at (14.97, -27.09, -14.75). (Replacing solvent molecule) Placed Na+ in aa at (11.87, 24.75, 10.66). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (11.35, -20.61, 6.20). Placed Cl- in aa at (17.19, 27.16, 12.95). (Replacing solvent molecule) Placed Na+ in aa at (15.64, 27.78, 15.57). (Replacing solvent molecule) Placed Na+ in aa at (15.41, -17.47, 8.09). (Replacing solvent molecule) (Replacing solvent molecule) Placed Cl- in aa at (16.84, 23.76, 17.80). (Replacing solvent molecule) Placed Na+ in aa at (16.50, 24.05, 20.63). Placed Cl- in aa at (10.67, -16.84, 10.75). (Replacing solvent molecule) Placed Cl- in aa at (-12.16, 17.55, 8.49). Done adding ions. > addions aa Na+ 10 Cl- 10 (Replacing solvent molecule) Placed Na+ in aa at (18.39, 20.80, 18.99). (Replacing solvent molecule) Placed Cl- in aa at (12.64, 20.42, 22.56). Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.89 -44.30 -44.14 45.94 38.74 37.56 sized: 93.11 83.70 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 (Replacing solvent molecule) Placed Na+ in aa at (12.50, 19.26, 19.79). (Replacing solvent molecule) Placed Cl- in aa at (13.79, 22.28, 17.97). (Replacing solvent molecule) Placed Na+ in aa at (12.75, 13.05, 22.80). (Replacing solvent molecule) Placed Cl- in aa at (13.16, 10.29, 22.81). (Replacing solvent molecule) Placed Na+ in aa at (-16.45, 17.87, 16.09). (Replacing solvent molecule) Placed Cl- in aa at (9.28, 17.88, 10.55). (Replacing solvent molecule) Placed Na+ in aa at (7.93, 20.09, 13.48). (Replacing solvent molecule) Placed Cl- in aa at (-14.11, 16.89, 12.24). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 47.19 37.85 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 charges: 201 sec grid build: 3 sec Volume = 5.10% of box, grid points 106900 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in aa at (24.27, 8.85, 15.57). (Replacing solvent molecule) Placed Cl- in aa at (-33.34, 11.26, 16.56). (Replacing solvent molecule) Placed Na+ in aa at (-41.56, 12.75, 9.28). (Replacing solvent molecule) Placed Cl- in aa at (21.42, 4.76, 17.91). (Replacing solvent molecule) Placed Na+ in aa at (-38.78, 10.39, 18.18). (Replacing solvent molecule) Placed Cl- in aa at (-36.58, 9.82, 20.69). grid build: 1 sec Volume = 4.78% of box, grid points 100307 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in aa at (-36.17, 13.95, 22.59). (Replacing solvent molecule) Placed Cl- in aa at (-35.45, 14.49, 18.57). (Replacing solvent molecule) Placed Na+ in aa at (-33.10, 13.32, 19.99). (Replacing solvent molecule) Placed Cl- in aa at (-33.72, 10.98, 24.57). (Replacing solvent molecule) Placed Na+ in aa at (-32.75, 9.83, 19.13). (Replacing solvent molecule) Placed Cl- in aa at (-10.57, 27.43, -10.32). (No solvent overlap) Placed Na+ in aa at (-6.79, 28.05, -10.42). (Replacing solvent molecule) Placed Cl- in aa at (-2.07, 23.93, -11.24). (Replacing solvent molecule) Placed Na+ in aa at (-3.65, 25.05, -8.58). (Replacing solvent molecule) Placed Cl- in aa at (-5.19, 29.33, -14.10). (Replacing solvent molecule) Placed Na+ in aa at (-1.10, 26.75, -14.66). (Replacing solvent molecule) Placed Cl- in aa at (4.58, 25.72, -8.37). (Replacing solvent molecule) Placed Na+ in aa at (-34.17, 7.13, 24.91). (Replacing solvent molecule) Placed Cl- in aa at (-30.72, 5.09, 22.56). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -49.35 -43.95 -38.42 45.83 40.01 38.10 sized: 78.65 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 5.13% of box, grid points 107564 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 157 sec (No solvent overlap) Placed Na+ in aa at (-5.62, -2.86, -8.92). (Replacing solvent molecule) Placed Cl- in aa at (25.91, 16.53, 14.91). (Replacing solvent molecule) Placed Na+ in aa at (29.17, 19.09, 11.92). (Replacing solvent molecule) Placed Cl- in aa at (-6.79, -0.14, -14.60). (Replacing solvent molecule) Placed Na+ in aa at (-9.81, 7.24, -15.04). (Replacing solvent molecule) Placed Cl- in aa at (-10.93, 5.56, -13.01). (Replacing solvent molecule) Placed Na+ in aa at (-13.06, 4.51, -10.83). (Replacing solvent molecule) Placed Cl- in aa at (-6.89, 8.66, -17.45). (Replacing solvent molecule) Placed Na+ in aa at (-6.08, 12.98, -17.77). (Replacing solvent molecule) Placed Cl- in aa at (-10.12, 13.59, -14.51). (Replacing solvent molecule) Placed Na+ in aa at (-12.39, 16.92, -9.44). (Replacing solvent molecule) Placed Cl- in aa at (-16.50, 18.06, -10.60). (Replacing solvent molecule) Placed Na+ in aa at (-7.42, 1.97, -13.02). (Replacing solvent molecule) Placed Cl- in aa at (-5.31, 5.84, -14.09). (Replacing solvent molecule) Placed Na+ in aa at (1.02, 3.58, -24.34). (Replacing solvent molecule) Placed Cl- in aa at (3.30, 6.69, -18.51). (Replacing solvent molecule) Placed Na+ in aa at (1.15, 3.74, -21.54). (Replacing solvent molecule) Placed Cl- in aa at (-2.12, 1.12, -24.65). (Replacing solvent molecule) Placed Na+ in aa at (-4.11, -1.21, -27.92). (Replacing solvent molecule) Placed Cl- in aa at (2.83, 6.52, -22.69). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -45.86 -38.92 42.72 38.64 38.02 sized: 92.38 82.14 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.92% of box, grid points 103203 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 209 sec (Replacing solvent molecule) Placed Na+ in aa at (18.81, -23.83, 5.03). (Replacing solvent molecule) Placed Cl- in aa at (17.31, 20.22, 13.92). (Replacing solvent molecule) Placed Na+ in aa at (12.85, 20.34, 9.90). (Replacing solvent molecule) Placed Cl- in aa at (9.95, 20.46, 10.18). (Replacing solvent molecule) Placed Na+ in aa at (5.88, 23.59, 6.20). (Replacing solvent molecule) Placed Cl- in aa at (6.91, 24.49, 9.35). (Replacing solvent molecule) Placed Na+ in aa at (8.00, 20.09, 13.22). (Replacing solvent molecule) Placed Cl- in aa at (3.59, 19.99, 6.82). (Replacing solvent molecule) Placed Na+ in aa at (2.19, 23.40, 6.51). (Replacing solvent molecule) Placed Cl- in aa at (2.32, 25.50, 9.99). (Replacing solvent molecule) Placed Na+ in aa at (2.10, 32.91, 11.95). (Replacing solvent molecule) Placed Cl- in aa at (2.54, 35.94, 12.45). (Replacing solvent molecule) Placed Na+ in aa at (2.53, 34.19, 9.27). (Replacing solvent molecule) Placed Cl- in aa at (4.78, 39.33, 6.09). (Replacing solvent molecule) Placed Na+ in aa at (6.41, 34.83, -0.58). (Replacing solvent molecule) Placed Cl- in aa at (-1.25, 32.89, 8.23). (Replacing solvent molecule) Placed Na+ in aa at (1.04, 38.46, 3.38). (Replacing solvent molecule) Placed Cl- in aa at (4.16, 38.00, -1.45). (Replacing solvent molecule) Placed Na+ in aa at (2.28, 34.88, -1.65). (Replacing solvent molecule) Placed Cl- in aa at (-0.76, 34.26, 3.03). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.05 -44.55 -40.53 42.16 47.12 37.47 sized: 88.95 83.45 87.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.91% of box, grid points 102897 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 166 sec (Replacing solvent molecule) Placed Na+ in aa at (-14.91, 17.49, 7.42). (Replacing solvent molecule) Placed Cl- in aa at (-17.12, 20.51, 5.89). (Replacing solvent molecule) Placed Na+ in aa at (-21.36, 14.96, 5.97). (Replacing solvent molecule) Placed Cl- in aa at (21.00, 21.21, 21.43). (Replacing solvent molecule) Placed Na+ in aa at (19.38, 25.41, 20.35). (Replacing solvent molecule) Placed Cl- in aa at (15.56, 31.66, 19.62). (Replacing solvent molecule) Placed Na+ in aa at (13.22, 26.83, 19.58). (Replacing solvent molecule) Placed Cl- in aa at (16.36, 25.79, 23.68). (Replacing solvent molecule) Placed Na+ in aa at (11.82, 30.79, 16.91). (Replacing solvent molecule) Placed Cl- in aa at (12.15, 25.25, 14.31). (Replacing solvent molecule) Placed Na+ in aa at (11.63, 22.97, 12.60). (Replacing solvent molecule) Placed Cl- in aa at (7.36, 24.53, 12.45). (Replacing solvent molecule) Placed Na+ in aa at (9.35, 23.70, 16.32). (Replacing solvent molecule) Placed Cl- in aa at (9.52, 25.22, 21.77). (Replacing solvent molecule) Placed Na+ in aa at (12.04, 29.15, 23.62). (Replacing solvent molecule) Placed Cl- in aa at (10.02, 26.59, 16.56). (Replacing solvent molecule) Placed Na+ in aa at (2.63, 24.45, 19.76). (Replacing solvent molecule) Placed Cl- in aa at (-2.07, 23.93, 15.31). (Replacing solvent molecule) Placed Na+ in aa at (-1.10, 26.75, 11.89). (Replacing solvent molecule) Placed Cl- in aa at (-1.65, 30.12, 11.64). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 47.19 37.85 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.88% of box, grid points 102266 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 191 sec (No solvent overlap) Placed Na+ in aa at (-19.35, 4.05, 22.58). (Replacing solvent molecule) Placed Cl- in aa at (-33.86, 15.40, 21.98). (Replacing solvent molecule) Placed Na+ in aa at (-37.22, 18.52, 22.05). (Replacing solvent molecule) Placed Cl- in aa at (-41.61, 20.24, 20.68). (Replacing solvent molecule) Placed Na+ in aa at (5.44, 24.60, -11.98). (Replacing solvent molecule) Placed Cl- in aa at (3.39, 26.93, -14.12). (Replacing solvent molecule) Placed Na+ in aa at (1.07, 26.39, -10.93). (Replacing solvent molecule) Placed Cl- in aa at (0.00, 29.65, -9.38). (Replacing solvent molecule) Placed Na+ in aa at (2.88, 29.33, -9.28). (Replacing solvent molecule) Placed Cl- in aa at (6.26, 4.93, 26.09). (Replacing solvent molecule) Placed Na+ in aa at (4.28, 8.68, 28.32). (Replacing solvent molecule) Placed Cl- in aa at (2.88, 6.33, 30.55). (Replacing solvent molecule) Placed Na+ in aa at (2.59, 1.19, 28.84). (Replacing solvent molecule) Placed Cl- in aa at (-44.46, 11.42, 11.89). (Replacing solvent molecule) Placed Na+ in aa at (-45.01, 14.79, 11.64). (Replacing solvent molecule) Placed Cl- in aa at (-43.46, 15.39, 9.44). (Replacing solvent molecule) Placed Na+ in aa at (-40.41, 14.61, 4.69). (Replacing solvent molecule) Placed Cl- in aa at (-38.87, 10.92, 7.00). (Replacing solvent molecule) Placed Na+ in aa at (-39.35, 14.05, -0.88). (Replacing solvent molecule) Placed Cl- in aa at (-40.05, 16.55, 2.89). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -52.80 -43.95 -38.42 45.83 40.01 38.34 sized: 75.20 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.28% of box, grid points 110669 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 221 sec (No solvent overlap) Placed Na+ in aa at (-21.89, 7.70, 7.86). (Replacing solvent molecule) Placed Cl- in aa at (-27.08, 8.65, 6.13). (Replacing solvent molecule) Placed Na+ in aa at (27.23, 5.52, 12.43). (Replacing solvent molecule) Placed Cl- in aa at (16.20, -13.23, 6.74). (Replacing solvent molecule) Placed Na+ in aa at (12.95, -7.39, 6.61). (Replacing solvent molecule) Placed Cl- in aa at (35.79, 8.75, -10.55). (Replacing solvent molecule) Placed Na+ in aa at (12.72, -10.07, 9.36). (Replacing solvent molecule) Placed Cl- in aa at (10.17, -6.48, 10.48). (Replacing solvent molecule) Placed Na+ in aa at (40.86, 7.49, -11.99). (Replacing solvent molecule) Placed Cl- in aa at (40.04, 5.34, -7.73). (Replacing solvent molecule) Placed Na+ in aa at (37.30, 5.00, -4.53). (Replacing solvent molecule) Placed Cl- in aa at (38.75, 4.80, -0.63). (Replacing solvent molecule) Placed Na+ in aa at (40.04, 11.11, -1.39). (Replacing solvent molecule) Placed Cl- in aa at (41.72, 10.73, -3.91). (Replacing solvent molecule) Placed Na+ in aa at (42.49, 9.09, -8.66). (Replacing solvent molecule) Placed Cl- in aa at (39.83, 11.06, -10.15). (Replacing solvent molecule) Placed Na+ in aa at (40.91, 5.90, 2.55). (Replacing solvent molecule) Placed Cl- in aa at (41.77, 9.05, 3.06). (Replacing solvent molecule) Placed Na+ in aa at (38.63, 10.73, 8.60). (Replacing solvent molecule) Placed Cl- in aa at (34.24, 12.45, 7.24). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.89 -44.30 -44.14 50.28 38.74 37.56 sized: 93.11 83.70 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.22% of box, grid points 109527 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 154 sec (Replacing solvent molecule) Placed Na+ in aa at (-20.70, 1.94, 23.80). (Replacing solvent molecule) Placed Cl- in aa at (12.55, 2.10, 15.89). (Replacing solvent molecule) Placed Na+ in aa at (9.96, -1.29, 14.25). (Replacing solvent molecule) Placed Cl- in aa at (4.37, -12.43, 24.51). (Replacing solvent molecule) Placed Na+ in aa at (8.62, -10.82, 15.73). (Replacing solvent molecule) Placed Cl- in aa at (11.48, -12.77, 13.65). (Replacing solvent molecule) Placed Na+ in aa at (8.04, -12.03, 19.65). (Replacing solvent molecule) Placed Cl- in aa at (8.60, -12.49, 22.95). (Replacing solvent molecule) Placed Na+ in aa at (8.32, -15.19, 27.87). (Replacing solvent molecule) Placed Cl- in aa at (8.42, -7.45, 19.14). (Replacing solvent molecule) Placed Na+ in aa at (8.72, -6.54, 15.18). (Replacing solvent molecule) Placed Cl- in aa at (9.69, -3.72, 11.75). (Replacing solvent molecule) Placed Na+ in aa at (9.09, -8.58, 24.14). (Replacing solvent molecule) Placed Cl- in aa at (7.86, -15.98, 18.43). (Replacing solvent molecule) Placed Na+ in aa at (10.56, -20.64, 18.99). (Replacing solvent molecule) Placed Cl- in aa at (9.23, -4.93, 23.69). (Replacing solvent molecule) Placed Na+ in aa at (4.89, -15.11, 23.05). (Replacing solvent molecule) Placed Cl- in aa at (3.30, -16.31, 21.32). (Replacing solvent molecule) Placed Na+ in aa at (5.44, -21.13, 23.49). (Replacing solvent molecule) Placed Cl- in aa at (7.87, -17.47, 24.95). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -45.86 -38.92 42.72 38.64 38.02 sized: 92.38 82.14 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.05% of box, grid points 105921 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 164 sec (Replacing solvent molecule) Placed Na+ in aa at (-14.05, 16.89, 11.98). (Replacing solvent molecule) Placed Cl- in aa at (-21.34, 12.10, 15.97). (Replacing solvent molecule) Placed Na+ in aa at (-25.12, 11.20, 16.31). (Replacing solvent molecule) Placed Cl- in aa at (-18.24, 17.44, 13.78). (Replacing solvent molecule) Placed Na+ in aa at (-18.28, 16.68, 17.47). (Replacing solvent molecule) Placed Cl- in aa at (5.58, 33.46, 10.14). (Replacing solvent molecule) Placed Na+ in aa at (6.84, 36.93, 11.78). (Replacing solvent molecule) Placed Cl- in aa at (-26.11, 11.84, 12.69). (Replacing solvent molecule) Placed Na+ in aa at (-28.44, 6.40, 12.14). (Replacing solvent molecule) Placed Cl- in aa at (-30.94, 5.12, 13.73). (Replacing solvent molecule) Placed Na+ in aa at (-22.08, 15.14, 13.25). (Replacing solvent molecule) Placed Cl- in aa at (-14.84, 17.50, 7.16). (Replacing solvent molecule) Placed Na+ in aa at (-20.97, 18.29, 8.02). (Replacing solvent molecule) Placed Cl- in aa at (-22.29, 15.65, 8.61). (Replacing solvent molecule) Placed Na+ in aa at (-26.32, 10.86, 8.51). (Replacing solvent molecule) Placed Cl- in aa at (-27.21, 15.08, 4.61). (Replacing solvent molecule) Placed Na+ in aa at (-27.30, 10.32, 3.37). (Replacing solvent molecule) Placed Cl- in aa at (-24.91, 11.24, -1.48). (Replacing solvent molecule) Placed Na+ in aa at (-26.63, 7.46, -3.44). (Replacing solvent molecule) Placed Cl- in aa at (-31.92, 10.18, 6.11). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.71 -44.55 -40.53 42.16 47.12 37.47 sized: 88.29 83.45 87.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.01% of box, grid points 105065 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 122 sec (Replacing solvent molecule) Placed Na+ in aa at (6.73, -31.87, -1.37). (Replacing solvent molecule) Placed Cl- in aa at (7.56, -23.68, 19.69). (Replacing solvent molecule) Placed Na+ in aa at (5.81, -26.30, 19.69). (Replacing solvent molecule) Placed Cl- in aa at (3.12, -24.41, 23.00). (Replacing solvent molecule) Placed Na+ in aa at (9.30, -22.10, 16.18). (Replacing solvent molecule) Placed Cl- in aa at (9.37, -19.56, 13.36). (Replacing solvent molecule) Placed Na+ in aa at (5.58, -16.40, 15.36). (Replacing solvent molecule) Placed Cl- in aa at (3.34, -18.86, 12.30). (Replacing solvent molecule) Placed Na+ in aa at (8.83, -19.64, 8.69). (Replacing solvent molecule) Placed Cl- in aa at (12.54, -17.89, 7.27). (Replacing solvent molecule) Placed Na+ in aa at (15.38, -17.16, 8.12). (Replacing solvent molecule) Placed Cl- in aa at (16.25, -21.69, 6.16). (Replacing solvent molecule) Placed Na+ in aa at (20.81, -26.87, 3.15). (Replacing solvent molecule) Placed Cl- in aa at (0.72, -40.06, -1.23). (Replacing solvent molecule) Placed Na+ in aa at (12.59, -25.38, 22.42). (Replacing solvent molecule) Placed Cl- in aa at (13.74, -23.52, 17.83). (Replacing solvent molecule) Placed Na+ in aa at (15.96, -22.90, 14.53). (Replacing solvent molecule) Placed Cl- in aa at (14.04, -23.10, 24.39). (Replacing solvent molecule) Placed Na+ in aa at (11.99, -16.65, 23.49). (Replacing solvent molecule) Placed Cl- in aa at (13.17, -18.97, 19.44). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -35.62 -47.85 -38.92 42.72 38.64 38.02 sized: 92.38 80.15 89.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.12% of box, grid points 107477 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 151 sec (No solvent overlap) Placed Na+ in aa at (-2.89, -27.30, 9.86). (Replacing solvent molecule) Placed Cl- in aa at (-5.23, -32.04, 15.32). (Replacing solvent molecule) Placed Na+ in aa at (-4.61, -33.52, 12.65). (Replacing solvent molecule) Placed Cl- in aa at (14.81, -6.99, 9.07). (Replacing solvent molecule) Placed Na+ in aa at (-6.58, -29.78, 14.88). (Replacing solvent molecule) Placed Cl- in aa at (-2.81, -31.44, 11.69). (Replacing solvent molecule) Placed Na+ in aa at (-0.71, -32.57, 7.99). (Replacing solvent molecule) Placed Cl- in aa at (-6.38, -35.19, 6.83). (Replacing solvent molecule) Placed Na+ in aa at (-11.32, -37.34, 4.77). (Replacing solvent molecule) Placed Cl- in aa at (43.61, 8.92, -12.83). (Replacing solvent molecule) Placed Na+ in aa at (45.11, 7.31, -7.89). (Replacing solvent molecule) Placed Cl- in aa at (-11.32, -38.65, 0.07). (Replacing solvent molecule) Placed Na+ in aa at (-8.96, -42.21, -1.98). (Replacing solvent molecule) Placed Cl- in aa at (-6.14, -43.90, -0.56). (Replacing solvent molecule) Placed Na+ in aa at (-14.14, 16.76, 12.07). (Replacing solvent molecule) Placed Cl- in aa at (-18.44, 14.49, 13.59). (Replacing solvent molecule) Placed Na+ in aa at (-21.43, 11.97, 16.07). (Replacing solvent molecule) Placed Cl- in aa at (-12.18, 17.42, 8.32). (Replacing solvent molecule) Placed Na+ in aa at (-20.51, 18.75, 4.98). (Replacing solvent molecule) Placed Cl- in aa at (-19.12, 16.39, 2.13). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.89 -51.69 -44.14 52.90 38.74 37.56 sized: 93.11 76.31 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.40% of box, grid points 113343 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 220 sec (Replacing solvent molecule) Placed Na+ in aa at (10.74, 23.06, 22.71). (Replacing solvent molecule) Placed Cl- in aa at (6.83, 22.99, 16.93). (Replacing solvent molecule) Placed Na+ in aa at (4.58, 25.72, 18.18). (Replacing solvent molecule) Placed Cl- in aa at (2.59, 31.23, 19.48). (Replacing solvent molecule) Placed Na+ in aa at (5.46, 31.77, 19.57). (Replacing solvent molecule) Placed Cl- in aa at (3.35, 29.49, 21.46). (Replacing solvent molecule) Placed Na+ in aa at (-1.47, 29.02, 21.24). (Replacing solvent molecule) Placed Cl- in aa at (9.50, 30.73, 21.98). (Replacing solvent molecule) Placed Na+ in aa at (12.88, 32.57, 20.51). (Replacing solvent molecule) Placed Cl- in aa at (10.58, 35.42, 17.91). (Replacing solvent molecule) Placed Na+ in aa at (8.09, 33.77, 19.78). (Replacing solvent molecule) Placed Cl- in aa at (0.64, 25.95, 21.56). (Replacing solvent molecule) Placed Na+ in aa at (4.15, 26.69, 25.24). (Replacing solvent molecule) Placed Cl- in aa at (7.57, 24.55, 25.52). (No solvent overlap) Placed Na+ in aa at (5.61, 21.56, 24.27). (Replacing solvent molecule) Placed Cl- in aa at (1.44, 25.57, 29.05). (Replacing solvent molecule) Placed Na+ in aa at (-0.67, 26.06, 27.05). (Replacing solvent molecule) Placed Cl- in aa at (13.28, 31.59, 22.97). (Replacing solvent molecule) Placed Na+ in aa at (9.78, 29.71, 30.16). (Replacing solvent molecule) Placed Cl- in aa at (13.80, 30.53, 29.45). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 47.19 37.95 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.97% of box, grid points 104246 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 195 sec (Replacing solvent molecule) Placed Na+ in aa at (-34.47, 10.83, 8.83). (Replacing solvent molecule) Placed Cl- in aa at (-39.98, 9.77, 0.77). (Replacing solvent molecule) Placed Na+ in aa at (-43.82, 7.46, 0.24). (Replacing solvent molecule) Placed Cl- in aa at (-36.72, 4.99, 7.79). (Replacing solvent molecule) Placed Na+ in aa at (-37.87, 9.34, -2.92). (Replacing solvent molecule) Placed Cl- in aa at (-36.17, 13.95, -3.96). (Replacing solvent molecule) Placed Na+ in aa at (-36.16, 7.14, 4.52). (Replacing solvent molecule) Placed Cl- in aa at (-40.58, 8.65, -3.96). (Replacing solvent molecule) Placed Na+ in aa at (-38.94, 18.04, -1.90). (Replacing solvent molecule) Placed Cl- in aa at (-42.32, 17.08, -2.62). (Replacing solvent molecule) Placed Na+ in aa at (-42.05, 17.59, 1.04). (Replacing solvent molecule) Placed Cl- in aa at (-41.17, 21.69, 0.65). (Replacing solvent molecule) Placed Na+ in aa at (-38.56, 20.12, 2.29). (Replacing solvent molecule) Placed Cl- in aa at (-37.01, 19.49, -0.32). (Replacing solvent molecule) Placed Na+ in aa at (-37.89, 16.44, -6.98). (Replacing solvent molecule) Placed Cl- in aa at (22.71, 17.08, 23.93). (Replacing solvent molecule) Placed Na+ in aa at (24.27, 15.90, 19.48). (Replacing solvent molecule) Placed Cl- in aa at (24.78, 19.66, 16.22). (Replacing solvent molecule) Placed Na+ in aa at (25.03, 14.16, 21.46). (Replacing solvent molecule) Placed Cl- in aa at (23.63, 12.67, 23.43). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -52.80 -43.95 -38.42 45.83 40.01 38.34 sized: 75.20 84.05 89.58 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.46% of box, grid points 114500 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 184 sec (No solvent overlap) Placed Na+ in aa at (-21.71, 0.45, 22.47). (Replacing solvent molecule) Placed Cl- in aa at (34.56, 14.17, -7.75). (Replacing solvent molecule) Placed Na+ in aa at (33.56, 15.47, -9.90). (Replacing solvent molecule) Placed Cl- in aa at (33.27, 17.71, -13.02). (Replacing solvent molecule) Placed Na+ in aa at (33.01, 16.73, -15.80). (Replacing solvent molecule) Placed Cl- in aa at (33.89, 9.93, -12.50). (Replacing solvent molecule) Placed Na+ in aa at (33.61, 9.43, -16.15). (Replacing solvent molecule) Placed Cl- in aa at (34.77, 14.03, -12.88). (Replacing solvent molecule) Placed Na+ in aa at (35.53, 6.96, -8.84). (Replacing solvent molecule) Placed Cl- in aa at (31.08, 9.07, -22.84). (Replacing solvent molecule) Placed Na+ in aa at (32.32, 20.10, -8.90). (Replacing solvent molecule) Placed Cl- in aa at (30.21, 23.03, -7.53). (Replacing solvent molecule) Placed Na+ in aa at (27.13, 25.22, -6.63). (Replacing solvent molecule) Placed Cl- in aa at (32.50, 3.97, -9.09). (Replacing solvent molecule) Placed Na+ in aa at (34.09, 5.12, -12.82). (Replacing solvent molecule) Placed Cl- in aa at (34.53, 5.01, -16.66). (Replacing solvent molecule) Placed Na+ in aa at (37.14, 5.19, -20.92). (Replacing solvent molecule) Placed Cl- in aa at (34.33, 12.58, -19.41). (Replacing solvent molecule) Placed Na+ in aa at (33.06, 11.99, -23.03). (Replacing solvent molecule) Placed Cl- in aa at (30.88, 21.90, -2.54). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.71 -44.55 -40.53 44.93 47.12 37.47 sized: 88.29 83.45 87.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 5.11% of box, grid points 107183 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 148 sec (Replacing solvent molecule) Placed Na+ in aa at (16.93, 26.38, 8.63). (Replacing solvent molecule) Placed Cl- in aa at (12.54, 28.09, 7.27). (No solvent overlap) Placed Na+ in aa at (10.38, 31.15, 8.08). (Replacing solvent molecule) Placed Cl- in aa at (8.49, 33.26, 6.94). (Replacing solvent molecule) Placed Na+ in aa at (5.47, 33.64, 10.26). (Replacing solvent molecule) Placed Cl- in aa at (3.34, 27.12, 12.30). (Replacing solvent molecule) Placed Na+ in aa at (1.02, 26.58, 15.49). (Replacing solvent molecule) Placed Cl- in aa at (0.59, 26.14, 21.42). (Replacing solvent molecule) Placed Na+ in aa at (2.21, 25.69, 10.11). (Replacing solvent molecule) Placed Cl- in aa at (-2.12, 24.12, 15.18). (Replacing solvent molecule) Placed Na+ in aa at (-6.30, 21.16, 21.40). (Replacing solvent molecule) Placed Cl- in aa at (3.01, 31.12, 8.34). (Replacing solvent molecule) Placed Na+ in aa at (-8.45, 24.11, 9.56). (Replacing solvent molecule) Placed Cl- in aa at (-1.03, 26.36, 8.45). (Replacing solvent molecule) Placed Na+ in aa at (-3.44, 26.74, 13.18). (Replacing solvent molecule) Placed Cl- in aa at (-13.81, 20.86, 11.67). (Replacing solvent molecule) Placed Na+ in aa at (-14.13, 17.35, 14.83). (Replacing solvent molecule) Placed Cl- in aa at (-11.04, 21.80, 24.05). (Replacing solvent molecule) Placed Na+ in aa at (0.93, 38.65, 3.50). (Replacing solvent molecule) Placed Cl- in aa at (7.50, -11.57, 11.92). Done adding ions. > > saveamberparm aa m2.topo m2.coords Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 15051 ) (no restraints) > > quit Quit charges: 158 sec (Replacing solvent molecule) Placed Na+ in aa at (-20.24, -5.09, 29.05). (Replacing solvent molecule) Placed Cl- in aa at (26.24, 12.85, 19.16). (Replacing solvent molecule) Placed Na+ in aa at (25.50, 12.00, 15.43). (Replacing solvent molecule) Placed Cl- in aa at (21.68, 14.32, 17.17). (Replacing solvent molecule) Placed Na+ in aa at (21.58, 19.04, 14.25). (Replacing solvent molecule) Placed Cl- in aa at (-24.28, -4.59, 30.15). (Replacing solvent molecule) Placed Na+ in aa at (-12.49, -31.20, -14.91). (Replacing solvent molecule) Placed Cl- in aa at (-11.94, -34.56, -14.66). (Replacing solvent molecule) Placed Na+ in aa at (-13.74, -33.82, -9.76). (Replacing solvent molecule) Placed Cl- in aa at (-6.03, -33.20, -17.63). (Replacing solvent molecule) Placed Na+ in aa at (-8.58, -35.82, -16.31). (Replacing solvent molecule) Placed Cl- in aa at (29.04, 9.20, 12.45). charges: 179 sec (Replacing solvent molecule) Placed Na+ in aa at (-11.71, 1.43, 31.17). (Replacing solvent molecule) Placed Na+ in aa at (31.56, 5.12, 10.44). (Replacing solvent molecule) Placed Cl- in aa at (-19.49, 4.09, 24.99). (Replacing solvent molecule) Placed Cl- in aa at (33.39, 1.52, 11.13). (Replacing solvent molecule) Placed Na+ in aa at (-21.27, 8.93, 24.12). (Replacing solvent molecule) Placed Cl- in aa at (-19.80, 12.92, 22.63). (Replacing solvent molecule) Placed Na+ in aa at (28.51, 7.66, 16.93). (Replacing solvent molecule) (Replacing solvent molecule) Placed Na+ in aa at (-21.60, 11.72, 18.95). Placed Cl- in aa at (27.90, 5.01, 15.91). (Replacing solvent molecule) Placed Cl- in aa at (-24.00, 9.95, 20.18). (Replacing solvent molecule) Placed Na+ in aa at (26.15, 1.18, 16.09). (Replacing solvent molecule) Placed Na+ in aa at (-22.55, 9.09, 17.89). (Replacing solvent molecule) Placed Cl- in aa at (-16.10, -32.67, -0.67). (Replacing solvent molecule) Placed Cl- in aa at (-23.68, 10.51, 13.94). (Replacing solvent molecule) Placed Na+ in aa at (-18.25, -30.14, -0.83). (Replacing solvent molecule) Placed Na+ in aa at (-23.89, 10.19, 9.65). (Replacing solvent molecule) Placed Cl- in aa at (-15.04, -33.33, -5.48). (Replacing solvent molecule) Placed Cl- in aa at (-22.16, 16.31, 18.04). Done adding ions. > > saveamberparm aa m1.topo m1.coords (Replacing solvent molecule) Placed Na+ in aa at (-22.77, 14.38, 16.06). Checking Unit. (Replacing solvent molecule) Placed Cl- in aa at (-25.51, 14.13, 16.07). Building topology. (Replacing solvent molecule) Placed Na+ in aa at (-25.61, 16.28, 18.07). Building atom parameters. (Replacing solvent molecule) Placed Cl- in aa at (-18.38, 10.58, 17.07). (Replacing solvent molecule) Placed Na+ in aa at (-16.31, 9.76, 20.02). Building bond parameters. Building angle parameters. (Replacing solvent molecule) Placed Cl- in aa at (-16.96, 10.69, 24.96). Building proper torsion parameters. (Replacing solvent molecule) Placed Na+ in aa at (-16.13, 13.19, 25.71). (Replacing solvent molecule) Placed Cl- in aa at (-18.16, 13.63, 31.96). (Replacing solvent molecule) Placed Na+ in aa at (-12.34, 13.56, 21.07). (Replacing solvent molecule) Placed Cl- in aa at (-10.33, 17.71, 19.48). Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 Done adding ions. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 > ** Warning: No sp2 improper torsion term for C*-CN-CB-CA addions aa Na+ 10 Cl- 10 atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 Adding 20 counter ions to "aa" using 1A grid ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -34.89 -51.69 -44.14 52.90 38.74 39.75 sized: 93.11 76.31 83.86 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14434 ) (no restraints) grid build: 1 sec Volume = 5.48% of box, grid points 114838 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges > > quit Quit charges: 179 sec (No solvent overlap) Placed Na+ in aa at (-2.39, 9.56, -0.73). (Replacing solvent molecule) Placed Cl- in aa at (-3.97, 29.49, 23.55). (Replacing solvent molecule) Placed Na+ in aa at (0.79, 30.63, 25.88). (Replacing solvent molecule) Placed Cl- in aa at (4.01, 29.38, 25.67). (Replacing solvent molecule) Placed Na+ in aa at (7.92, 28.33, 25.08). (Replacing solvent molecule) Placed Cl- in aa at (9.28, 32.17, 16.50). (Replacing solvent molecule) Placed Na+ in aa at (12.55, 33.68, 17.01). (Replacing solvent molecule) Placed Cl- in aa at (14.31, 32.44, 13.67). (Replacing solvent molecule) Placed Na+ in aa at (13.16, 33.28, 9.54). (Replacing solvent molecule) Placed Cl- in aa at (11.38, -20.48, 6.37). (Replacing solvent molecule) Placed Na+ in aa at (8.04, -20.32, 6.11). (Replacing solvent molecule) Placed Cl- in aa at (7.55, -17.52, 5.71). (Replacing solvent molecule) Placed Na+ in aa at (14.19, -24.16, 8.18). (Replacing solvent molecule) Placed Cl- in aa at (18.75, -23.83, 5.29). (Replacing solvent molecule) Placed Na+ in aa at (20.12, -21.48, 3.23). (Replacing solvent molecule) Placed Cl- in aa at (23.72, -21.08, 7.23). (Replacing solvent molecule) Placed Na+ in aa at (18.53, -25.96, 7.12). (Replacing solvent molecule) Placed Cl- in aa at (20.19, -29.96, 3.04). (Replacing solvent molecule) Placed Na+ in aa at (22.47, -30.68, -0.67). (Replacing solvent molecule) Placed Cl- in aa at (27.14, -29.55, -6.98). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -33.39 -44.44 -38.73 43.98 47.19 37.95 sized: 94.61 83.56 89.27 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.07% of box, grid points 106353 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 163 sec (Replacing solvent molecule) Placed Na+ in aa at (-21.30, 14.97, 5.71). (Replacing solvent molecule) Placed Cl- in aa at (-22.84, 19.67, 5.65). (Replacing solvent molecule) Placed Na+ in aa at (-28.93, 19.99, 6.82). (Replacing solvent molecule) Placed Cl- in aa at (-19.03, 16.53, 2.03). (Replacing solvent molecule) Placed Na+ in aa at (-23.68, 16.27, 1.78). (Replacing solvent molecule) Placed Cl- in aa at (10.76, -16.71, 10.65). (Replacing solvent molecule) Placed Na+ in aa at (10.08, -19.39, 16.30). (Replacing solvent molecule) Placed Cl- in aa at (-16.43, 8.42, -16.32). (Replacing solvent molecule) Placed Na+ in aa at (15.00, -15.65, 11.83). (Replacing solvent molecule) Placed Cl- in aa at (13.09, -16.63, 13.67). (Replacing solvent molecule) Placed Na+ in aa at (9.34, -13.81, 16.24). (Replacing solvent molecule) Placed Cl- in aa at (12.62, -12.30, 16.75). (Replacing solvent molecule) Placed Na+ in aa at (10.17, -10.49, 20.36). (Replacing solvent molecule) Placed Cl- in aa at (13.34, -14.39, 22.71). (Replacing solvent molecule) Placed Na+ in aa at (14.33, -7.14, 12.18). (Replacing solvent molecule) Placed Cl- in aa at (13.16, -5.15, 9.99). (Replacing solvent molecule) Placed Na+ in aa at (14.29, -3.72, 12.17). (Replacing solvent molecule) Placed Cl- in aa at (16.53, -1.25, 15.23). (Replacing solvent molecule) Placed Na+ in aa at (19.27, 1.48, 13.32). (Replacing solvent molecule) Placed Cl- in aa at (18.26, -6.12, 12.19). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: -0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.71 -44.55 -40.53 44.93 47.12 37.47 sized: 88.29 83.45 87.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.18% of box, grid points 108637 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 141 sec (No solvent overlap) Placed Na+ in aa at (22.61, -15.44, -14.73). (Replacing solvent molecule) Placed Cl- in aa at (24.31, -13.87, -20.07). (Replacing solvent molecule) Placed Na+ in aa at (19.31, -15.30, -20.55). (Replacing solvent molecule) Placed Cl- in aa at (17.69, -16.26, -23.91). (Replacing solvent molecule) Placed Na+ in aa at (17.62, -16.73, -27.79). (Replacing solvent molecule) Placed Cl- in aa at (15.57, -13.11, -26.95). (Replacing solvent molecule) Placed Na+ in aa at (18.28, -11.77, -26.51). (Replacing solvent molecule) Placed Cl- in aa at (19.21, -21.52, -26.25). (Replacing solvent molecule) Placed Na+ in aa at (15.12, -21.98, -24.78). (Replacing solvent molecule) Placed Cl- in aa at (13.43, -22.42, -20.35). (Replacing solvent molecule) Placed Na+ in aa at (15.40, -25.48, -20.66). (Replacing solvent molecule) Placed Cl- in aa at (18.75, -23.83, -21.26). (Replacing solvent molecule) Placed Na+ in aa at (22.66, -22.86, -22.91). (Replacing solvent molecule) Placed Cl- in aa at (20.36, -28.44, -18.06). (Replacing solvent molecule) Placed Na+ in aa at (17.25, -25.78, -12.37). (Replacing solvent molecule) Placed Cl- in aa at (24.85, -16.94, -16.69). (Replacing solvent molecule) Placed Na+ in aa at (27.17, -13.66, -16.20). (Replacing solvent molecule) Placed Cl- in aa at (16.33, -28.99, 10.35). (Replacing solvent molecule) Placed Na+ in aa at (13.47, -29.20, 6.48). (Replacing solvent molecule) Placed Cl- in aa at (11.48, -27.70, 8.28). Done adding ions. > > saveamberparm aa m4.topo m4.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. charges: 159 sec (Replacing solvent molecule) Placed Na+ in aa at (2.01, 9.78, -27.79). (Replacing solvent molecule) Placed Cl- in aa at (-13.34, 10.21, 21.02). (No solvent overlap) Placed Na+ in aa at (-9.89, 11.31, 19.86). (Replacing solvent molecule) Placed Cl- in aa at (-14.35, 16.74, 25.56). Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA (Replacing solvent molecule) atoms are: CG CE2 CD2 CE3 Placed Na+ in aa at (-17.89, 19.53, 28.54). ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 (Replacing solvent molecule) total 1539 improper torsions applied Placed Cl- in aa at (2.35, 11.38, -33.69). Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Replacing solvent molecule) Placed Na+ in aa at (4.75, 11.60, -32.01). (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14442 ) (no restraints) (Replacing solvent molecule) Placed Cl- in aa at (3.04, 7.81, -31.51). (Replacing solvent molecule) Placed Na+ in aa at (-12.82, 18.37, 21.94). (Replacing solvent molecule) Placed Cl- in aa at (-7.51, 14.03, 21.29). (Replacing solvent molecule) Placed Na+ in aa at (0.29, 7.11, -34.79). (Replacing solvent molecule) Placed Cl- in aa at (-14.01, 19.90, 33.50). (Replacing solvent molecule) Placed Na+ in aa at (-14.93, 17.36, 33.80). (Replacing solvent molecule) Placed Cl- in aa at (-17.55, 18.90, 38.35). (Replacing solvent molecule) Placed Na+ in aa at (-18.93, 16.19, 35.70). (Replacing solvent molecule) Placed Cl- in aa at (-18.53, 13.59, 36.24). (Replacing solvent molecule) Placed Na+ in aa at (-16.06, 13.88, 38.83). (Replacing solvent molecule) Placed Cl- in aa at (-11.69, 18.80, 29.67). (Replacing solvent molecule) Placed Na+ in aa at (-7.56, 16.42, 29.27). (Replacing solvent molecule) Placed Cl- in aa at (-7.92, 14.49, 31.08). Done adding ions. > > saveamberparm aa m3.topo m3.coords Checking Unit. >WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A > quit Quit -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 15292 ) (no restraints) > > quit Quit charges: 109 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.31, -27.69, 13.00). (Replacing solvent molecule) Placed Cl- in aa at (-2.41, -29.18, 13.32). (Replacing solvent molecule) Placed Na+ in aa at (-0.08, -32.03, 10.65). (Replacing solvent molecule) Placed Cl- in aa at (1.37, -36.06, 14.05). (Replacing solvent molecule) Placed Na+ in aa at (4.48, -35.61, 11.11). (Replacing solvent molecule) Placed Cl- in aa at (1.81, -33.41, 7.14). (Replacing solvent molecule) Placed Na+ in aa at (0.54, -34.00, 3.52). (Replacing solvent molecule) Placed Cl- in aa at (2.25, -31.96, 13.67). (Replacing solvent molecule) Placed Na+ in aa at (1.04, -30.52, 16.65). (Replacing solvent molecule) Placed Cl- in aa at (-3.18, -36.48, 1.43). (Replacing solvent molecule) Placed Na+ in aa at (6.84, -31.68, 12.16). (Replacing solvent molecule) Placed Cl- in aa at (8.71, -35.67, 9.55). (Replacing solvent molecule) Placed Na+ in aa at (6.20, -35.12, 8.51). (Replacing solvent molecule) Placed Cl- in aa at (3.07, -24.39, 14.46). (Replacing solvent molecule) Placed Na+ in aa at (3.49, -22.47, 12.18). (Replacing solvent molecule) Placed Cl- in aa at (3.45, -19.05, 12.17). (Replacing solvent molecule) Placed Na+ in aa at (8.00, -25.90, 13.22). (Replacing solvent molecule) Placed Cl- in aa at (9.35, -28.10, 10.29). (Replacing solvent molecule) Placed Na+ in aa at (8.43, -27.98, 7.65). (Replacing solvent molecule) Placed Cl- in aa at (9.41, -22.28, 16.06). Done adding ions. > > saveamberparm aa m5.topo m5.coords Checking Unit. WARNING: There is a bond of 4.392637 angstroms between: ------- .R.A and .R.A -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1539 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CARG 1 HEM 1 NPRO 1 WAT 14712 ) (no restraints) > > quit Quit