log started: Wed Jul 16 16:46:07 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m1_invacuo.topo m1_invacuo.coords Checking Unit. WARNING: There is a bond of 4.012864 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > quit Quit log started: Wed Jul 16 16:46:41 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m1_invacuo.topo m1_invacuo.coords Checking Unit. WARNING: There is a bond of 4.012864 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > quit Quit log started: Wed Jul 16 16:47:01 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 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m1_invacuo.topo m1_invacuo.coords Checking Unit. WARNING: There is a bond of 4.012864 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.347095 to meet diagonal cut criterion Solute vdw bounding box: 49.395 77.186 63.566 Total bounding box for atom centers: 109.517 109.517 109.517 (box expansion for 'iso' is 53.0%) 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: 674920.792 A^3 (oct) Total mass 370174.104 amu, Density 0.911 g/cc Added 17514 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -40.72 -43.36 -41.01 39.81 40.47 40.66 sized: 87.28 84.64 86.99 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.12% of box, grid points 86351 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 82 sec (Replacing solvent molecule) Placed Cl- in aa at (-23.00, -15.18, -4.69). (Replacing solvent molecule) Placed Cl- in aa at (-1.29, 32.95, 8.37). (Replacing solvent molecule) Placed Cl- in aa at (-22.63, 18.58, 21.73). 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: -40.04 -42.68 -40.33 39.13 40.74 39.98 sized: 87.96 85.32 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.49% of box, grid points 94117 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 117 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.60, -26.37, -1.52). (Replacing solvent molecule) Placed Cl- in aa at (-23.35, -8.70, -2.40). (Replacing solvent molecule) Placed Na+ in aa at (-6.66, -34.55, -1.44). (Replacing solvent molecule) Placed Cl- in aa at (-5.88, -30.55, -3.49). (Replacing solvent molecule) Placed Na+ in aa at (-2.16, -27.94, -3.59). (Replacing solvent molecule) Placed Cl- in aa at (31.87, 0.39, 8.74). (Replacing solvent molecule) Placed Na+ in aa at (35.17, 1.53, 6.36). (Replacing solvent molecule) Placed Cl- in aa at (9.45, -9.33, 10.06). (Replacing solvent molecule) Placed Na+ in aa at (5.21, -6.85, 10.36). (Replacing solvent molecule) Placed Cl- in aa at (4.61, -8.00, 13.76). (Replacing solvent molecule) Placed Na+ in aa at (2.98, -7.72, 16.05). (Replacing solvent molecule) Placed Cl- in aa at (5.42, -5.37, 20.06). (Replacing solvent molecule) Placed Na+ in aa at (7.38, -4.90, 9.71). (Replacing solvent molecule) Placed Cl- in aa at (9.22, -0.46, 11.51). (Replacing solvent molecule) Placed Na+ in aa at (9.55, 2.30, 8.37). (Replacing solvent molecule) Placed Cl- in aa at (7.97, -3.09, 16.66). (Replacing solvent molecule) Placed Na+ in aa at (8.49, -7.57, 19.15). (Replacing solvent molecule) Placed Cl- in aa at (-17.64, -1.20, 25.55). (Replacing solvent molecule) Placed Na+ in aa at (-20.35, 2.33, 27.46). (Replacing solvent molecule) Placed Cl- in aa at (-23.51, -0.31, 26.59). 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: -40.04 -42.68 -40.33 42.96 40.74 39.98 sized: 87.96 85.32 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.58% of box, grid points 96144 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 123 sec (No solvent overlap) Placed Na+ in aa at (-1.04, -26.68, -12.33). (Replacing solvent molecule) Placed Cl- in aa at (-1.39, -24.66, -16.49). (Replacing solvent molecule) Placed Na+ in aa at (-4.60, -24.32, -17.57). (Replacing solvent molecule) Placed Cl- in aa at (-6.10, -21.92, -20.33). (Replacing solvent molecule) Placed Na+ in aa at (-0.43, -21.81, -21.74). (Replacing solvent molecule) Placed Cl- in aa at (-0.95, -19.74, -18.09). (Replacing solvent molecule) Placed Na+ in aa at (-0.84, -16.93, -19.16). (Replacing solvent molecule) Placed Cl- in aa at (1.69, -18.99, -20.17). (Replacing solvent molecule) Placed Na+ in aa at (2.97, -15.97, -21.99). (Replacing solvent molecule) Placed Cl- in aa at (5.20, -15.36, -25.28). (Replacing solvent molecule) Placed Na+ in aa at (6.28, -18.00, -13.86). (Replacing solvent molecule) Placed Cl- in aa at (10.04, -19.32, -10.12). (Replacing solvent molecule) Placed Na+ in aa at (9.38, -22.22, -10.36). (Replacing solvent molecule) Placed Cl- in aa at (7.38, -21.38, -14.23). (Replacing solvent molecule) Placed Na+ in aa at (11.90, -21.17, -16.02). (Replacing solvent molecule) Placed Cl- in aa at (12.82, -25.58, -16.52). (Replacing solvent molecule) Placed Na+ in aa at (13.49, -29.13, -20.20). (Replacing solvent molecule) Placed Cl- in aa at (12.31, -28.01, -10.91). (Replacing solvent molecule) Placed Na+ in aa at (9.31, -28.04, -16.13). (Replacing solvent molecule) Placed Cl- in aa at (13.08, -33.50, -19.18). 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: -40.04 -42.68 -40.33 42.96 40.74 39.98 sized: 87.96 85.32 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.69% of box, grid points 98336 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 98 sec (Replacing solvent molecule) Placed Na+ in aa at (25.52, 12.07, 15.30). (Replacing solvent molecule) Placed Cl- in aa at (6.66, -25.60, -18.89). (Replacing solvent molecule) Placed Na+ in aa at (8.39, -27.92, -18.76). (Replacing solvent molecule) Placed Cl- in aa at (7.10, -30.24, -18.43). (Replacing solvent molecule) Placed Na+ in aa at (10.19, -30.27, -17.81). (Replacing solvent molecule) Placed Cl- in aa at (25.06, 14.23, 21.33). (Replacing solvent molecule) Placed Na+ in aa at (28.48, -1.33, -27.91). (Replacing solvent molecule) Placed Cl- in aa at (12.06, -27.04, -21.53). (Replacing solvent molecule) Placed Na+ in aa at (13.46, -22.35, -20.47). (Replacing solvent molecule) Placed Cl- in aa at (12.61, -18.01, -19.27). (Replacing solvent molecule) Placed Na+ in aa at (12.89, -13.03, -19.84). (Replacing solvent molecule) Placed Cl- in aa at (13.33, -12.26, -25.25). (Replacing solvent molecule) Placed Na+ in aa at (14.68, -26.25, -24.53). (Replacing solvent molecule) Placed Cl- in aa at (15.15, -21.91, -24.90). (Replacing solvent molecule) Placed Na+ in aa at (11.14, -13.87, -26.07). (Replacing solvent molecule) Placed Cl- in aa at (17.69, -30.59, -23.02). (Replacing solvent molecule) Placed Na+ in aa at (11.12, -31.24, -23.71). (Replacing solvent molecule) Placed Cl- in aa at (8.80, -29.65, -24.64). (Replacing solvent molecule) Placed Na+ in aa at (3.35, -27.55, -22.72). (Replacing solvent molecule) Placed Cl- in aa at (0.30, -26.15, -23.72). 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: -40.04 -42.68 -40.33 42.96 40.74 39.98 sized: 87.96 85.32 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.82% of box, grid points 101070 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 132 sec (No solvent overlap) Placed Na+ in aa at (9.96, 12.32, 21.67). (Replacing solvent molecule) Placed Cl- in aa at (18.06, -8.12, -22.16). (Replacing solvent molecule) Placed Na+ in aa at (20.48, -10.92, -20.77). (Replacing solvent molecule) Placed Cl- in aa at (33.74, 3.62, 5.02). (Replacing solvent molecule) Placed Na+ in aa at (32.86, -0.29, 5.84). (Replacing solvent molecule) Placed Cl- in aa at (31.13, -1.67, -3.21). (Replacing solvent molecule) Placed Na+ in aa at (29.06, 2.76, -3.57). (Replacing solvent molecule) Placed Cl- in aa at (29.79, -4.48, 6.38). (Replacing solvent molecule) Placed Na+ in aa at (32.50, -2.22, 0.28). (Replacing solvent molecule) Placed Cl- in aa at (35.97, 0.59, -0.96). (Replacing solvent molecule) Placed Na+ in aa at (34.57, -5.36, -6.56). (Replacing solvent molecule) Placed Cl- in aa at (10.40, -30.79, -13.17). (Replacing solvent molecule) Placed Na+ in aa at (13.33, -35.25, -11.97). (Replacing solvent molecule) Placed Cl- in aa at (4.02, 23.87, -17.44). (Replacing solvent molecule) Placed Na+ in aa at (5.85, 23.66, -20.22). (Replacing solvent molecule) Placed Cl- in aa at (7.57, 28.54, -20.97). (Replacing solvent molecule) Placed Na+ in aa at (13.46, 23.64, -20.47). (Replacing solvent molecule) Placed Cl- in aa at (16.03, 25.72, -23.04). (Replacing solvent molecule) Placed Na+ in aa at (1.69, 27.00, -20.17). (Replacing solvent molecule) Placed Cl- in aa at (-2.58, 26.14, -23.08). 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: -40.04 -43.04 -40.33 43.76 40.74 39.98 sized: 87.96 84.96 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.94% of box, grid points 103570 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 130 sec (No solvent overlap) Placed Na+ in aa at (3.96, 4.96, -23.33). (Replacing solvent molecule) Placed Cl- in aa at (9.89, -4.41, 8.46). (No solvent overlap) Placed Na+ in aa at (6.96, -6.04, 6.67). (Replacing solvent molecule) Placed Cl- in aa at (0.50, -10.94, 16.93). (Replacing solvent molecule) Placed Na+ in aa at (0.56, -12.75, 19.52). (Replacing solvent molecule) Placed Cl- in aa at (0.03, -16.27, 17.04). (Replacing solvent molecule) Placed Na+ in aa at (1.79, -13.35, 15.90). (Replacing solvent molecule) Placed Cl- in aa at (3.13, -10.93, 16.09). (Replacing solvent molecule) Placed Na+ in aa at (8.69, -10.93, 15.74). (Replacing solvent molecule) Placed Cl- in aa at (10.13, -10.42, 20.50). (Replacing solvent molecule) Placed Na+ in aa at (11.18, -7.96, 19.12). (Replacing solvent molecule) Placed Cl- in aa at (13.45, -6.40, 15.44). (Replacing solvent molecule) Placed Na+ in aa at (14.25, -3.65, 12.31). (Replacing solvent molecule) Placed Cl- in aa at (11.51, -4.63, 21.43). (Replacing solvent molecule) Placed Na+ in aa at (13.46, 0.65, 19.35). (Replacing solvent molecule) Placed Cl- in aa at (17.50, -10.27, 7.66). (Replacing solvent molecule) Placed Na+ in aa at (19.53, -18.60, 2.46). (Replacing solvent molecule) Placed Cl- in aa at (15.28, 2.78, 24.52). (Replacing solvent molecule) Placed Na+ in aa at (13.49, -6.14, 19.63). (Replacing solvent molecule) Placed Cl- in aa at (18.77, -0.77, 18.44). 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: -40.04 -43.04 -40.33 43.76 40.74 39.98 sized: 87.96 84.96 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.02% of box, grid points 105290 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 133 sec (Replacing solvent molecule) Placed Na+ in aa at (-14.81, -29.09, -3.80). (Replacing solvent molecule) Placed Cl- in aa at (-19.85, -25.50, -4.12). (Replacing solvent molecule) Placed Na+ in aa at (-18.40, -23.21, -2.15). (Replacing solvent molecule) Placed Cl- in aa at (18.41, -19.35, -1.35). (Replacing solvent molecule) Placed Na+ in aa at (20.29, -17.00, -3.21). (Replacing solvent molecule) Placed Cl- in aa at (21.80, -18.74, -7.56). (Replacing solvent molecule) Placed Na+ in aa at (23.84, -14.86, -6.63). (Replacing solvent molecule) Placed Cl- in aa at (25.70, -14.45, -4.17). (Replacing solvent molecule) Placed Na+ in aa at (25.13, -14.74, -0.96). (Replacing solvent molecule) Placed Cl- in aa at (24.71, -16.66, 1.31). (Replacing solvent molecule) Placed Na+ in aa at (21.96, -15.92, 2.84). (Replacing solvent molecule) Placed Cl- in aa at (17.72, -16.18, 2.51). (Replacing solvent molecule) Placed Na+ in aa at (12.63, -21.01, 2.63). (Replacing solvent molecule) Placed Cl- in aa at (11.40, -20.41, 6.24). (Replacing solvent molecule) Placed Na+ in aa at (8.07, -20.25, 5.98). (Replacing solvent molecule) Placed Cl- in aa at (9.36, -21.52, 3.84). (Replacing solvent molecule) Placed Na+ in aa at (7.05, -23.72, 1.35). (Replacing solvent molecule) Placed Cl- in aa at (3.35, -27.55, 3.83). (Replacing solvent molecule) Placed Na+ in aa at (2.16, -22.52, 6.65). (Replacing solvent molecule) Placed Cl- in aa at (3.46, -22.40, 12.32). 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: -40.04 -43.04 -40.33 43.76 40.74 39.98 sized: 87.96 84.96 87.67 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.09% of box, grid points 106680 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 101 sec (Replacing solvent molecule) Placed Na+ in aa at (-1.93, 10.90, 35.25). (Replacing solvent molecule) Placed Cl- in aa at (1.06, 9.49, 37.08). (Replacing solvent molecule) Placed Na+ in aa at (19.52, 2.72, 22.96). (Replacing solvent molecule) Placed Cl- in aa at (3.29, -23.63, 0.36). (Replacing solvent molecule) Placed Na+ in aa at (5.67, -24.25, -0.95). (Replacing solvent molecule) Placed Cl- in aa at (9.22, -23.46, -1.76). (Replacing solvent molecule) Placed Na+ in aa at (11.18, -23.35, -8.20). (Replacing solvent molecule) Placed Cl- in aa at (-12.24, -27.34, 0.09). (Replacing solvent molecule) Placed Na+ in aa at (-12.30, -29.88, 2.92). (Replacing solvent molecule) Placed Cl- in aa at (-7.87, -31.30, 4.57). (Replacing solvent molecule) Placed Na+ in aa at (9.89, -27.40, -4.82). (Replacing solvent molecule) Placed Cl- in aa at (8.26, -27.51, -9.80). (Replacing solvent molecule) Placed Na+ in aa at (7.06, -31.65, -10.44). (Replacing solvent molecule) Placed Cl- in aa at (9.45, -32.33, -3.21). (Replacing solvent molecule) Placed Na+ in aa at (7.57, -34.68, -1.35). (Replacing solvent molecule) Placed Cl- in aa at (10.96, -34.07, -7.56). (Replacing solvent molecule) Placed Na+ in aa at (13.00, -30.19, -6.63). (Replacing solvent molecule) Placed Cl- in aa at (13.12, -28.08, -3.16). (Replacing solvent molecule) Placed Na+ in aa at (14.39, -33.60, -6.32). (Replacing solvent molecule) Placed Cl- in aa at (14.85, -32.16, -10.49). Done adding ions. > > saveamberparm aa m1.topo m1.coords Checking Unit. WARNING: There is a bond of 4.012864 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 WAT 17375 ) (no restraints) > > quit Quit log started: Wed Jul 16 17:12:05 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HIS, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HIE Joining HIE - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m2_invacuo.topo m2_invacuo.coords Checking Unit. WARNING: There is a bond of 4.012864 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.334833 to meet diagonal cut criterion Solute vdw bounding box: 47.624 77.217 63.615 Total bounding box for atom centers: 109.253 109.253 109.253 (box expansion for 'iso' is 56.7%) 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: 670105.519 A^3 (oct) Total mass 368012.184 amu, Density 0.912 g/cc Added 17394 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -40.52 -43.68 -40.28 39.97 40.27 41.40 sized: 87.48 84.32 87.72 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.12% of box, grid points 86315 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 83 sec (Replacing solvent molecule) Placed Cl- in aa at (-23.30, -15.13, -4.59). (Replacing solvent molecule) Placed Cl- in aa at (-22.60, 16.77, 23.90). (Replacing solvent molecule) Placed Cl- in aa at (-7.74, 32.89, 14.02). 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: -39.84 -43.00 -39.60 39.29 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.49% of box, grid points 94188 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 86 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.90, -26.32, -1.41). (Replacing solvent molecule) Placed Cl- in aa at (-23.66, -8.64, -2.30). (Replacing solvent molecule) Placed Na+ in aa at (-21.68, -10.77, 2.94). (Replacing solvent molecule) Placed Cl- in aa at (-19.47, -17.59, -0.59). (Replacing solvent molecule) Placed Na+ in aa at (-21.48, -18.55, 3.76). (Replacing solvent molecule) Placed Cl- in aa at (-20.21, -17.96, 7.38). (Replacing solvent molecule) Placed Na+ in aa at (-19.93, -12.97, 6.82). (Replacing solvent molecule) Placed Cl- in aa at (-24.25, -12.79, 7.05). (Replacing solvent molecule) Placed Na+ in aa at (-17.54, -20.15, 11.35). (Replacing solvent molecule) Placed Cl- in aa at (-18.60, -24.03, 8.16). (Replacing solvent molecule) Placed Na+ in aa at (-17.80, -26.83, 11.94). (Replacing solvent molecule) Placed Cl- in aa at (-16.78, -22.96, 14.65). (Replacing solvent molecule) Placed Na+ in aa at (-13.42, -20.45, 20.33). (Replacing solvent molecule) Placed Cl- in aa at (-13.90, -23.52, 25.11). (Replacing solvent molecule) Placed Na+ in aa at (29.76, 0.90, -27.27). (Replacing solvent molecule) Placed Cl- in aa at (-23.01, -16.15, 3.59). (Replacing solvent molecule) Placed Na+ in aa at (-19.36, -22.29, 6.18). (Replacing solvent molecule) Placed Cl- in aa at (-14.62, -19.34, 16.55). (Replacing solvent molecule) Placed Na+ in aa at (-12.17, -23.82, 16.86). (Replacing solvent molecule) Placed Cl- in aa at (31.57, 0.45, 8.84). 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: -39.84 -43.00 -39.60 39.36 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.58% of box, grid points 96144 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 88 sec (Replacing solvent molecule) Placed Na+ in aa at (26.85, 9.40, 14.55). (Replacing solvent molecule) Placed Cl- in aa at (17.76, -8.06, -22.06). (Replacing solvent molecule) Placed Na+ in aa at (20.18, -10.87, -20.67). (Replacing solvent molecule) Placed Cl- in aa at (-14.04, -2.20, 25.06). (Replacing solvent molecule) Placed Na+ in aa at (-15.55, -2.65, 27.44). (Replacing solvent molecule) Placed Cl- in aa at (-20.44, -2.42, 27.25). (Replacing solvent molecule) Placed Na+ in aa at (-23.44, 0.83, 29.57). (Replacing solvent molecule) Placed Cl- in aa at (-22.78, 3.72, 29.81). (Replacing solvent molecule) Placed Na+ in aa at (-21.17, 0.10, 25.86). (Replacing solvent molecule) Placed Cl- in aa at (-20.65, 2.39, 27.56). (Replacing solvent molecule) Placed Na+ in aa at (-19.77, 6.49, 27.18). (Replacing solvent molecule) Placed Cl- in aa at (-22.80, 9.35, 18.04). (Replacing solvent molecule) Placed Na+ in aa at (-23.93, 10.77, 14.08). (Replacing solvent molecule) Placed Cl- in aa at (-27.62, 7.69, 14.65). (Replacing solvent molecule) Placed Na+ in aa at (-24.88, 5.47, 11.78). (Replacing solvent molecule) Placed Cl- in aa at (24.28, -8.87, -22.57). (Replacing solvent molecule) Placed Na+ in aa at (-30.58, 12.01, 11.86). (Replacing solvent molecule) Placed Cl- in aa at (-26.02, 14.43, 12.40). (Replacing solvent molecule) Placed Na+ in aa at (-25.25, 5.60, 18.96). (Replacing solvent molecule) Placed Cl- in aa at (-25.95, 1.62, 22.86). 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: -39.84 -43.00 -39.60 39.36 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.68% of box, grid points 98170 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 91 sec (Replacing solvent molecule) Placed Na+ in aa at (-0.32, -25.16, -12.89). (Replacing solvent molecule) Placed Cl- in aa at (-0.92, -21.55, -15.92). (Replacing solvent molecule) Placed Na+ in aa at (-4.90, -24.26, -17.46). (Replacing solvent molecule) Placed Cl- in aa at (-3.57, -26.96, -14.52). (Replacing solvent molecule) Placed Na+ in aa at (-1.25, -19.68, -17.99). (Replacing solvent molecule) Placed Cl- in aa at (-6.40, -21.87, -20.22). (Replacing solvent molecule) Placed Na+ in aa at (-11.72, -21.60, -20.57). (Replacing solvent molecule) Placed Cl- in aa at (-13.54, -24.50, -23.85). (Replacing solvent molecule) Placed Na+ in aa at (-10.14, -22.73, -22.94). (Replacing solvent molecule) Placed Cl- in aa at (-14.76, -24.25, -17.26). (Replacing solvent molecule) Placed Na+ in aa at (-14.04, -25.19, -14.77). (Replacing solvent molecule) Placed Cl- in aa at (-14.88, -14.85, -18.32). (Replacing solvent molecule) Placed Na+ in aa at (-10.80, -15.57, -20.61). (Replacing solvent molecule) Placed Cl- in aa at (-9.40, -19.84, -22.84). (Replacing solvent molecule) Placed Na+ in aa at (-15.82, -19.67, -17.80). (Replacing solvent molecule) Placed Cl- in aa at (-18.65, -21.65, -10.41). (Replacing solvent molecule) Placed Na+ in aa at (-18.57, -26.59, -0.86). (Replacing solvent molecule) Placed Cl- in aa at (-20.19, -20.96, 2.73). (Replacing solvent molecule) Placed Na+ in aa at (-20.76, -26.98, 5.13). (Replacing solvent molecule) Placed Cl- in aa at (-15.34, -17.44, -20.60). 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: -39.84 -43.00 -39.60 39.36 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.75% of box, grid points 99706 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 93 sec (No solvent overlap) Placed Na+ in aa at (9.16, 13.00, 22.40). (Replacing solvent molecule) Placed Cl- in aa at (-19.37, -29.34, 2.27). (Replacing solvent molecule) Placed Na+ in aa at (-15.13, -30.54, 3.64). (Replacing solvent molecule) Placed Cl- in aa at (-16.52, -31.66, 8.28). (Replacing solvent molecule) Placed Na+ in aa at (15.95, 10.02, 20.16). (Replacing solvent molecule) Placed Cl- in aa at (12.88, 10.42, 22.79). (No solvent overlap) Placed Na+ in aa at (11.16, 8.00, 20.40). (Replacing solvent molecule) Placed Cl- in aa at (-12.97, -30.91, 0.14). (Replacing solvent molecule) Placed Na+ in aa at (-9.60, -33.08, 0.70). (Replacing solvent molecule) Placed Cl- in aa at (12.31, 5.04, 20.66). (Replacing solvent molecule) Placed Na+ in aa at (-15.32, -33.21, -5.51). (Replacing solvent molecule) Placed Cl- in aa at (-15.08, -31.70, -3.02). (Replacing solvent molecule) Placed Na+ in aa at (-20.88, -31.14, -1.65). (Replacing solvent molecule) Placed Cl- in aa at (-17.96, -29.72, -4.06). (Replacing solvent molecule) Placed Na+ in aa at (-14.60, -28.99, -0.85). (Replacing solvent molecule) Placed Cl- in aa at (-7.10, -31.81, -0.90). (Replacing solvent molecule) Placed Na+ in aa at (-5.63, -36.52, -2.95). (Replacing solvent molecule) Placed Cl- in aa at (17.20, -10.21, 7.77). (Replacing solvent molecule) Placed Na+ in aa at (15.30, -12.05, 11.83). (Replacing solvent molecule) Placed Cl- in aa at (12.47, -9.82, 9.50). 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: -39.84 -44.31 -39.60 39.36 40.68 40.72 sized: 88.16 83.69 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.85% of box, grid points 101668 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 128 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.18, -30.50, -3.39). (Replacing solvent molecule) Placed Cl- in aa at (-9.92, -34.64, -8.15). (Replacing solvent molecule) Placed Na+ in aa at (-11.95, -32.01, -12.19). (Replacing solvent molecule) Placed Cl- in aa at (-14.93, -31.32, -11.82). (Replacing solvent molecule) Placed Na+ in aa at (-16.13, -29.94, -6.84). (Replacing solvent molecule) Placed Cl- in aa at (-14.01, -33.70, -9.79). (Replacing solvent molecule) Placed Na+ in aa at (-12.76, -31.07, -14.94). (Replacing solvent molecule) Placed Cl- in aa at (6.59, -24.03, -16.30). (Replacing solvent molecule) Placed Na+ in aa at (-10.24, -36.68, -2.17). (Replacing solvent molecule) Placed Cl- in aa at (-7.74, -36.09, 0.74). (Replacing solvent molecule) Placed Na+ in aa at (-8.17, -31.25, 4.67). (Replacing solvent molecule) Placed Cl- in aa at (-11.98, -32.20, 7.49). (Replacing solvent molecule) Placed Na+ in aa at (-11.20, -34.23, 4.42). (Replacing solvent molecule) Placed Cl- in aa at (-14.25, -36.81, 1.30). (Replacing solvent molecule) Placed Na+ in aa at (-17.38, -34.76, 4.31). (Replacing solvent molecule) Placed Cl- in aa at (-3.67, -42.30, 0.01). (Replacing solvent molecule) Placed Na+ in aa at (-7.78, -36.85, 4.43). (Replacing solvent molecule) Placed Cl- in aa at (-6.63, -34.94, 6.98). (Replacing solvent molecule) Placed Na+ in aa at (-8.53, -37.01, -11.01). (Replacing solvent molecule) Placed Cl- in aa at (-10.35, -32.46, -14.39). 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: -39.84 -50.09 -39.60 39.36 40.68 40.72 sized: 88.16 77.91 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.92% of box, grid points 103081 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 102 sec (No solvent overlap) Placed Na+ in aa at (4.16, 4.91, -22.60). (Replacing solvent molecule) Placed Cl- in aa at (-12.54, -27.28, 0.20). (Replacing solvent molecule) Placed Na+ in aa at (-24.88, -17.53, -1.49). (Replacing solvent molecule) Placed Cl- in aa at (-22.06, 3.84, 14.23). (Replacing solvent molecule) Placed Na+ in aa at (-20.19, 2.04, 16.00). (Replacing solvent molecule) Placed Cl- in aa at (-18.60, -1.04, 21.43). (Replacing solvent molecule) Placed Na+ in aa at (-22.45, 1.07, 21.66). (Replacing solvent molecule) Placed Cl- in aa at (-21.42, 2.64, 19.62). (Replacing solvent molecule) Placed Na+ in aa at (-16.49, 1.24, 19.55). (Replacing solvent molecule) Placed Cl- in aa at (-19.08, -1.20, 17.25). (Replacing solvent molecule) Placed Na+ in aa at (-17.38, -4.81, 18.16). (Replacing solvent molecule) Placed Cl- in aa at (-21.27, -35.82, 0.49). (Replacing solvent molecule) Placed Na+ in aa at (-18.49, -36.42, 0.37). (Replacing solvent molecule) Placed Cl- in aa at (-19.18, -6.55, 22.56). (Replacing solvent molecule) Placed Na+ in aa at (-18.78, -9.14, 23.11). (Replacing solvent molecule) Placed Cl- in aa at (-18.42, -9.11, 18.83). (Replacing solvent molecule) Placed Na+ in aa at (-21.31, -4.58, 21.54). (Replacing solvent molecule) Placed Cl- in aa at (-8.98, -37.79, 6.75). (Replacing solvent molecule) Placed Na+ in aa at (-8.86, -35.69, 10.22). (Replacing solvent molecule) Placed Cl- in aa at (-7.73, -34.25, 12.41). 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: -39.84 -50.09 -39.60 39.36 40.68 40.72 sized: 88.16 77.91 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.93% of box, grid points 103298 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 98 sec (Replacing solvent molecule) Placed Na+ in aa at (-12.76, -31.07, 11.62). (Replacing solvent molecule) Placed Cl- in aa at (-5.68, -16.33, -18.27). (Replacing solvent molecule) Placed Na+ in aa at (-1.14, -16.87, -19.06). (Replacing solvent molecule) Placed Cl- in aa at (1.39, -18.93, -20.06). (Replacing solvent molecule) Placed Na+ in aa at (1.86, -22.47, -19.80). (Replacing solvent molecule) Placed Cl- in aa at (3.71, -24.44, -23.66). (Replacing solvent molecule) Placed Na+ in aa at (4.95, -20.32, -23.76). (Replacing solvent molecule) Placed Cl- in aa at (6.59, -1.04, 23.53). (Replacing solvent molecule) Placed Na+ in aa at (5.94, -2.53, 29.17). (Replacing solvent molecule) Placed Cl- in aa at (3.26, -1.44, 32.11). (Replacing solvent molecule) Placed Na+ in aa at (0.92, 3.68, 31.68). (Replacing solvent molecule) Placed Cl- in aa at (8.14, 6.16, 29.25). (Replacing solvent molecule) Placed Na+ in aa at (12.75, 6.49, 27.18). (Replacing solvent molecule) Placed Cl- in aa at (2.60, 6.46, 30.53). (Replacing solvent molecule) Placed Na+ in aa at (4.30, 2.86, 31.43). (Replacing solvent molecule) Placed Cl- in aa at (8.71, -0.25, 26.69). (Replacing solvent molecule) Placed Na+ in aa at (12.51, -2.53, 23.41). (Replacing solvent molecule) Placed Cl- in aa at (13.16, 0.70, 19.46). (Replacing solvent molecule) Placed Na+ in aa at (14.98, 2.84, 24.63). (Replacing solvent molecule) Placed Cl- in aa at (17.34, 6.77, 25.68). Done adding ions. > > saveamberparm aa m2.topo m2.coords Checking Unit. WARNING: There is a bond of 4.012864 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 WAT 17254 ) (no restraints) > > quit Quit log started: Wed Jul 16 17:31:33 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 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m3_invacuo.topo m3_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.303026 to meet diagonal cut criterion Solute vdw bounding box: 46.869 77.722 63.236 Total bounding box for atom centers: 108.994 108.994 108.994 (box expansion for 'iso' is 60.9%) 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: 665397.102 A^3 (oct) Total mass 365237.720 amu, Density 0.911 g/cc Added 17240 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -40.26 -42.41 -40.92 39.60 41.58 40.78 sized: 87.74 85.59 87.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.03% of box, grid points 84446 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 80 sec (Replacing solvent molecule) Placed Cl- in aa at (-22.41, -14.05, -7.10). (Replacing solvent molecule) Placed Cl- in aa at (-3.35, 29.80, 6.72). (Replacing solvent molecule) Placed Cl- in aa at (31.73, 0.34, 9.04). 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: -39.58 -41.73 -40.24 39.52 40.90 40.10 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.39% of box, grid points 92079 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 84 sec (Replacing solvent molecule) Placed Na+ in aa at (-6.95, -31.92, -0.71). (Replacing solvent molecule) Placed Cl- in aa at (9.25, -1.62, 21.41). (Replacing solvent molecule) Placed Na+ in aa at (11.92, -4.10, 18.59). (Replacing solvent molecule) Placed Cl- in aa at (14.54, -3.32, 15.60). (Replacing solvent molecule) Placed Na+ in aa at (15.00, 1.03, 15.22). (Replacing solvent molecule) Placed Cl- in aa at (11.36, -4.69, 21.73). (Replacing solvent molecule) Placed Na+ in aa at (14.07, -1.15, 21.63). (Replacing solvent molecule) Placed Cl- in aa at (13.31, 0.59, 19.65). (Replacing solvent molecule) Placed Na+ in aa at (26.03, -4.69, -26.39). (Replacing solvent molecule) Placed Cl- in aa at (21.56, -8.66, -22.49). (Replacing solvent molecule) Placed Na+ in aa at (13.04, 10.31, 22.98). (Replacing solvent molecule) Placed Cl- in aa at (11.26, -20.47, 6.54). (Replacing solvent molecule) Placed Na+ in aa at (9.22, -21.57, 4.14). (Replacing solvent molecule) Placed Cl- in aa at (5.70, -22.39, 6.63). (No solvent overlap) Placed Na+ in aa at (4.42, -21.73, 1.76). (Replacing solvent molecule) Placed Cl- in aa at (6.90, -23.77, 1.65). (Replacing solvent molecule) Placed Na+ in aa at (11.49, -24.90, -0.93). (Replacing solvent molecule) Placed Cl- in aa at (9.74, -27.46, -4.52). (Replacing solvent molecule) Placed Na+ in aa at (10.64, -26.68, -8.66). (Replacing solvent molecule) Placed Cl- in aa at (10.05, -27.58, -12.61). 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: -39.58 -41.73 -40.24 39.52 40.90 40.10 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.45% of box, grid points 93254 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 86 sec (Replacing solvent molecule) Placed Na+ in aa at (-2.31, -27.99, -3.29). (Replacing solvent molecule) Placed Cl- in aa at (-21.94, -10.59, -3.04). (Replacing solvent molecule) Placed Na+ in aa at (-21.53, -10.88, 3.13). (Replacing solvent molecule) Placed Cl- in aa at (-20.02, -15.54, 5.72). (Replacing solvent molecule) Placed Na+ in aa at (-24.10, -12.90, 7.25). (Replacing solvent molecule) Placed Cl- in aa at (-25.09, -11.74, 12.22). (Replacing solvent molecule) Placed Na+ in aa at (-21.84, -9.94, 13.85). (Replacing solvent molecule) Placed Cl- in aa at (-20.72, -8.26, 11.81). (Replacing solvent molecule) Placed Na+ in aa at (-19.54, -5.14, 10.41). (Replacing solvent molecule) Placed Cl- in aa at (-24.32, -8.76, 7.31). (Replacing solvent molecule) Placed Na+ in aa at (-21.70, -9.09, 7.78). (Replacing solvent molecule) Placed Cl- in aa at (-21.37, -13.91, 11.18). (Replacing solvent molecule) Placed Na+ in aa at (-17.06, -12.16, 12.02). (Replacing solvent molecule) Placed Cl- in aa at (-19.58, -10.56, 20.94). (Replacing solvent molecule) Placed Na+ in aa at (-19.17, -6.19, 19.93). (Replacing solvent molecule) Placed Cl- in aa at (-19.85, -2.64, 23.60). (Replacing solvent molecule) Placed Na+ in aa at (-20.29, -2.53, 27.44). (Replacing solvent molecule) Placed Cl- in aa at (-17.98, -3.32, 15.60). (Replacing solvent molecule) Placed Na+ in aa at (-18.37, -7.13, 12.61). (Replacing solvent molecule) Placed Cl- in aa at (-18.79, -9.05, 14.88). 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: -39.58 -41.73 -40.24 39.52 40.90 40.10 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.53% of box, grid points 94949 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 88 sec (Replacing solvent molecule) Placed Na+ in aa at (32.16, 9.85, -7.25). (Replacing solvent molecule) Placed Cl- in aa at (31.81, 13.34, -6.39). (Replacing solvent molecule) Placed Na+ in aa at (29.65, 18.46, -6.60). (Replacing solvent molecule) Placed Cl- in aa at (35.46, 7.95, -4.63). (Replacing solvent molecule) Placed Na+ in aa at (34.43, 9.93, -0.90). (Replacing solvent molecule) Placed Cl- in aa at (34.88, 12.96, -0.40). (Replacing solvent molecule) Placed Na+ in aa at (27.56, 16.11, 4.69). (Replacing solvent molecule) Placed Cl- in aa at (29.92, 15.30, 1.63). (Replacing solvent molecule) Placed Na+ in aa at (31.49, 15.09, -1.17). (Replacing solvent molecule) Placed Cl- in aa at (23.54, 21.84, 5.96). (Replacing solvent molecule) Placed Na+ in aa at (23.27, 26.04, 3.90). (Replacing solvent molecule) Placed Cl- in aa at (21.30, 27.77, 4.81). (Replacing solvent molecule) Placed Na+ in aa at (34.06, 3.95, -6.60). (Replacing solvent molecule) Placed Cl- in aa at (34.16, 9.59, 2.92). (Replacing solvent molecule) Placed Na+ in aa at (32.94, 10.19, 6.54). (Replacing solvent molecule) Placed Cl- in aa at (27.70, 18.54, -4.34). (Replacing solvent molecule) Placed Na+ in aa at (26.50, 15.38, -3.20). (Replacing solvent molecule) Placed Cl- in aa at (26.35, 20.13, 2.46). (Replacing solvent molecule) Placed Na+ in aa at (23.78, 19.56, -1.22). (Replacing solvent molecule) Placed Cl- in aa at (25.82, 23.43, -3.51). 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: -39.58 -41.73 -40.24 43.25 40.90 40.10 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.63% of box, grid points 97019 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 91 sec (No solvent overlap) Placed Na+ in aa at (12.42, 17.27, -5.24). (Replacing solvent molecule) Placed Cl- in aa at (20.73, 18.94, -23.10). (Replacing solvent molecule) Placed Na+ in aa at (18.64, 20.69, -14.57). (Replacing solvent molecule) Placed Cl- in aa at (17.07, 27.18, -13.43). (Replacing solvent molecule) Placed Na+ in aa at (15.51, 27.80, -10.82). (Replacing solvent molecule) Placed Cl- in aa at (13.19, 26.54, -3.57). (Replacing solvent molecule) Placed Na+ in aa at (13.10, 26.85, -6.81). (Replacing solvent molecule) Placed Cl- in aa at (11.70, 30.81, -9.47). (Replacing solvent molecule) Placed Na+ in aa at (11.92, 29.17, -2.76). (Replacing solvent molecule) Placed Cl- in aa at (9.52, 26.33, -1.81). (Replacing solvent molecule) Placed Na+ in aa at (15.19, 25.97, 0.16). (Replacing solvent molecule) Placed Cl- in aa at (13.82, 27.34, 3.11). (Replacing solvent molecule) Placed Na+ in aa at (7.92, 25.69, 6.28). (Replacing solvent molecule) Placed Cl- in aa at (4.77, 28.03, 4.62). (Replacing solvent molecule) Placed Na+ in aa at (10.62, 26.72, 1.14). (Replacing solvent molecule) Placed Cl- in aa at (2.47, 31.25, -6.90). (Replacing solvent molecule) Placed Na+ in aa at (3.23, 29.51, -4.93). (Replacing solvent molecule) Placed Cl- in aa at (9.38, 30.75, -4.40). (Replacing solvent molecule) Placed Na+ in aa at (5.37, 24.68, -2.75). (Replacing solvent molecule) Placed Cl- in aa at (1.83, 28.02, -2.95). 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: -39.58 -41.73 -40.24 43.25 40.90 40.10 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.68% of box, grid points 98055 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 93 sec (No solvent overlap) Placed Na+ in aa at (6.42, 13.27, 25.76). (Replacing solvent molecule) Placed Cl- in aa at (8.65, 16.28, 28.76). (Replacing solvent molecule) Placed Na+ in aa at (4.61, 17.56, 26.32). (Replacing solvent molecule) Placed Cl- in aa at (1.78, 19.26, 24.91). (Replacing solvent molecule) Placed Na+ in aa at (-7.90, 15.62, 35.20). (Replacing solvent molecule) Placed Cl- in aa at (16.72, 23.77, -8.59). (Replacing solvent molecule) Placed Na+ in aa at (-2.10, 18.32, 27.55). (Replacing solvent molecule) Placed Cl- in aa at (-0.12, 6.67, 30.61). (Replacing solvent molecule) Placed Na+ in aa at (0.42, 10.19, 33.09). (Replacing solvent molecule) Placed Cl- in aa at (-6.08, 19.33, 31.83). (Replacing solvent molecule) Placed Na+ in aa at (-5.30, 16.40, 34.07). (Replacing solvent molecule) Placed Cl- in aa at (-2.08, 10.85, 35.55). (Replacing solvent molecule) Placed Na+ in aa at (-0.62, 8.62, 35.13). (Replacing solvent molecule) Placed Cl- in aa at (4.82, 7.72, 36.63). (Replacing solvent molecule) Placed Na+ in aa at (7.97, 33.79, -6.60). (Replacing solvent molecule) Placed Cl- in aa at (-5.13, 15.14, 36.82). (Replacing solvent molecule) Placed Na+ in aa at (-3.60, 9.22, 39.17). (Replacing solvent molecule) Placed Cl- in aa at (-20.72, 14.74, 25.09). (Replacing solvent molecule) Placed Na+ in aa at (-21.84, 13.06, 27.13). (Replacing solvent molecule) Placed Cl- in aa at (-4.09, 6.52, 37.00). 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: -39.58 -41.73 -40.24 43.25 41.58 46.96 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.82% of box, grid points 101037 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 96 sec (Replacing solvent molecule) Placed Na+ in aa at (0.95, 3.41, 29.07). (Replacing solvent molecule) Placed Cl- in aa at (9.30, 3.27, 26.94). (Replacing solvent molecule) Placed Na+ in aa at (12.03, 2.28, 27.75). (Replacing solvent molecule) Placed Cl- in aa at (15.51, 4.81, 29.01). (Replacing solvent molecule) Placed Na+ in aa at (15.13, 2.73, 24.82). (Replacing solvent molecule) Placed Cl- in aa at (14.73, -1.26, 25.84). (Replacing solvent molecule) Placed Na+ in aa at (20.07, -6.94, 16.49). (Replacing solvent molecule) Placed Cl- in aa at (16.94, -10.30, 16.08). (Replacing solvent molecule) Placed Na+ in aa at (18.08, -6.11, 12.62). (Replacing solvent molecule) Placed Cl- in aa at (17.57, -6.15, 9.77). (Replacing solvent molecule) Placed Na+ in aa at (13.97, -0.28, 11.42). (Replacing solvent molecule) Placed Cl- in aa at (18.78, -0.64, 12.03). (Replacing solvent molecule) Placed Na+ in aa at (19.60, -4.48, 9.00). (Replacing solvent molecule) Placed Cl- in aa at (17.59, -8.81, 10.45). (Replacing solvent molecule) Placed Na+ in aa at (17.46, -13.89, 11.16). (Replacing solvent molecule) Placed Cl- in aa at (17.91, -13.26, 4.86). (Replacing solvent molecule) Placed Na+ in aa at (20.89, -14.99, 9.04). (Replacing solvent molecule) Placed Cl- in aa at (17.33, -17.55, 6.14). (Replacing solvent molecule) Placed Na+ in aa at (17.57, -16.24, 2.80). (Replacing solvent molecule) Placed Cl- in aa at (11.49, -1.91, 12.35). 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: -39.58 -41.73 -40.24 43.25 41.58 46.96 sized: 88.42 86.27 87.76 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.89% of box, grid points 102543 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 97 sec (Replacing solvent molecule) Placed Na+ in aa at (3.27, 3.96, -27.22). (Replacing solvent molecule) Placed Cl- in aa at (21.10, -15.51, 13.68). (Replacing solvent molecule) Placed Na+ in aa at (23.46, -19.07, 11.63). (Replacing solvent molecule) Placed Cl- in aa at (24.73, -16.92, 10.03). (Replacing solvent molecule) Placed Na+ in aa at (24.82, -16.02, 13.93). (Replacing solvent molecule) Placed Cl- in aa at (22.87, -5.39, 14.48). (Replacing solvent molecule) Placed Na+ in aa at (20.97, -1.99, 20.16). (Replacing solvent molecule) Placed Cl- in aa at (20.22, 0.09, 22.15). (Replacing solvent molecule) Placed Na+ in aa at (28.33, -13.15, 7.59). (Replacing solvent molecule) Placed Cl- in aa at (21.88, -8.07, 18.65). (Replacing solvent molecule) Placed Na+ in aa at (23.36, -10.22, 22.72). (Replacing solvent molecule) Placed Cl- in aa at (0.65, 5.75, -27.48). (Replacing solvent molecule) Placed Na+ in aa at (1.64, 9.59, -23.63). (Replacing solvent molecule) Placed Cl- in aa at (0.36, 12.00, -22.60). (Replacing solvent molecule) Placed Na+ in aa at (-3.41, 13.15, -20.67). (Replacing solvent molecule) Placed Cl- in aa at (-5.13, 15.14, -16.28). (Replacing solvent molecule) Placed Na+ in aa at (-5.33, 14.09, -10.89). (Replacing solvent molecule) Placed Cl- in aa at (27.05, -13.64, 10.52). (Replacing solvent molecule) Placed Na+ in aa at (24.51, -8.36, 18.14). (Replacing solvent molecule) Placed Cl- in aa at (24.62, -7.38, 21.92). Done adding ions. > > saveamberparm aa m3.topo m3.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 total 1507 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 CTHR 1 HEM 1 NHIE 1 WAT 17100 ) (no restraints) > > quit Quit log started: Thu Jul 17 10:23:42 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m4_invacuo.topo m4_invacuo.coords Checking Unit. WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.339281 to meet diagonal cut criterion Solute vdw bounding box: 47.884 78.526 64.956 Total bounding box for atom centers: 110.668 110.668 110.668 (box expansion for 'iso' is 57.6%) 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: 696241.935 A^3 (oct) Total mass 383830.232 amu, Density 0.915 g/cc Added 18272 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -39.45 -43.23 -41.37 40.33 37.38 40.48 sized: 88.55 84.77 86.63 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.03% of box, grid points 84426 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 87 sec (Replacing solvent molecule) Placed Cl- in aa at (-21.89, -10.70, -3.33). (Replacing solvent molecule) Placed Cl- in aa at (-5.42, 32.23, 10.23). (Replacing solvent molecule) Placed Cl- in aa at (-19.77, -16.60, -7.61). 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: -38.77 -42.55 -40.69 39.65 40.02 39.80 sized: 89.23 85.45 87.31 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.39% of box, grid points 91986 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 116 sec (Replacing solvent molecule) Placed Na+ in aa at (-11.40, -29.82, -4.99). (Replacing solvent molecule) Placed Cl- in aa at (-24.27, 14.12, 20.29). (Replacing solvent molecule) Placed Na+ in aa at (26.08, -4.80, -26.68). (Replacing solvent molecule) Placed Cl- in aa at (23.37, -5.85, -23.92). (Replacing solvent molecule) Placed Na+ in aa at (21.62, -8.77, -22.78). (Replacing solvent molecule) Placed Cl- in aa at (26.17, -10.24, -20.79). (Replacing solvent molecule) Placed Na+ in aa at (-6.75, -34.72, -1.43). (Replacing solvent molecule) Placed Cl- in aa at (-10.12, -30.78, -0.79). (Replacing solvent molecule) Placed Na+ in aa at (-8.69, -26.54, -1.51). (Replacing solvent molecule) Placed Cl- in aa at (-3.72, -32.14, -4.08). (Replacing solvent molecule) Placed Na+ in aa at (-5.97, -30.72, -3.49). (Replacing solvent molecule) Placed Cl- in aa at (-5.05, -18.93, -20.12). (Replacing solvent molecule) Placed Na+ in aa at (-5.47, -16.55, -18.37). (Replacing solvent molecule) Placed Cl- in aa at (2.19, 25.40, -16.43). (Replacing solvent molecule) Placed Na+ in aa at (-4.08, -15.43, -23.02). (Replacing solvent molecule) Placed Cl- in aa at (0.25, -15.85, -21.47). (Replacing solvent molecule) Placed Na+ in aa at (-1.48, -24.83, -16.48). (Replacing solvent molecule) Placed Cl- in aa at (-8.32, -14.24, -24.38). (Replacing solvent molecule) Placed Na+ in aa at (-10.59, -15.79, -20.71). (Replacing solvent molecule) Placed Cl- in aa at (-14.67, -15.08, -18.42). 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: -38.77 -42.55 -40.69 39.65 40.02 39.80 sized: 89.23 85.45 87.31 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.42% of box, grid points 92689 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 117 sec (No solvent overlap) Placed Na+ in aa at (6.23, -4.55, -18.69). (Replacing solvent molecule) Placed Cl- in aa at (-1.04, -19.91, -18.09). (Replacing solvent molecule) Placed Na+ in aa at (-0.15, -19.13, -22.23). (Replacing solvent molecule) Placed Cl- in aa at (3.27, -21.75, -22.22). (Replacing solvent molecule) Placed Na+ in aa at (3.46, -26.10, -19.59). (Replacing solvent molecule) Placed Cl- in aa at (5.18, -31.01, -21.80). (Replacing solvent molecule) Placed Na+ in aa at (18.47, -3.06, -32.83). (Replacing solvent molecule) Placed Cl- in aa at (18.34, -6.21, -27.71). (Replacing solvent molecule) Placed Na+ in aa at (16.26, -6.09, -29.60). (Replacing solvent molecule) Placed Cl- in aa at (20.30, -5.54, -31.46). (Replacing solvent molecule) Placed Na+ in aa at (24.68, -7.49, -31.47). (Replacing solvent molecule) Placed Cl- in aa at (11.64, -6.24, -28.82). (Replacing solvent molecule) Placed Na+ in aa at (8.30, -5.09, -32.03). (Replacing solvent molecule) Placed Cl- in aa at (6.67, -6.34, -28.96). (Replacing solvent molecule) Placed Na+ in aa at (4.19, -7.34, -30.35). (Replacing solvent molecule) Placed Cl- in aa at (3.46, -3.11, -32.87). (Replacing solvent molecule) Placed Na+ in aa at (1.84, -2.38, -30.42). (Replacing solvent molecule) Placed Cl- in aa at (6.55, -10.00, -33.98). (Replacing solvent molecule) Placed Na+ in aa at (13.09, 10.19, 22.69). (Replacing solvent molecule) Placed Cl- in aa at (14.87, 7.24, 25.24). 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: -38.77 -42.55 -41.77 39.65 40.02 39.80 sized: 89.23 85.45 86.23 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.54% of box, grid points 95242 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 121 sec (Replacing solvent molecule) Placed Na+ in aa at (-2.02, 10.73, 35.26). (Replacing solvent molecule) Placed Cl- in aa at (1.84, -25.37, -17.15). (No solvent overlap) Placed Na+ in aa at (0.23, -24.55, -13.77). (Replacing solvent molecule) Placed Cl- in aa at (21.47, -1.48, 10.79). (Replacing solvent molecule) Placed Na+ in aa at (16.43, 0.96, 7.23). (Replacing solvent molecule) Placed Cl- in aa at (14.16, -3.82, 12.31). (Replacing solvent molecule) Placed Na+ in aa at (19.14, 1.38, 13.46). (Replacing solvent molecule) Placed Cl- in aa at (22.59, 0.04, 16.79). (Replacing solvent molecule) Placed Na+ in aa at (20.93, -1.88, 8.03). (Replacing solvent molecule) Placed Cl- in aa at (15.67, -2.75, 4.33). (Replacing solvent molecule) Placed Na+ in aa at (15.26, -4.51, 6.88). (Replacing solvent molecule) Placed Cl- in aa at (17.64, -8.93, 10.15). (Replacing solvent molecule) Placed Na+ in aa at (16.35, -9.77, 12.48). (Replacing solvent molecule) Placed Cl- in aa at (16.29, 2.70, 10.28). (Replacing solvent molecule) Placed Na+ in aa at (14.02, -0.39, 11.13). (Replacing solvent molecule) Placed Cl- in aa at (12.43, -3.83, 6.39). (Replacing solvent molecule) Placed Na+ in aa at (14.77, -6.96, 9.11). (Replacing solvent molecule) Placed Cl- in aa at (15.03, -15.01, 9.47). (Replacing solvent molecule) Placed Na+ in aa at (11.20, -14.03, 10.89). (Replacing solvent molecule) Placed Cl- in aa at (10.13, -6.45, 10.53). 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: -38.77 -42.55 -41.77 39.65 40.02 43.05 sized: 89.23 85.45 86.23 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.56% of box, grid points 95723 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 124 sec (Replacing solvent molecule) Placed Na+ in aa at (32.22, 9.73, -7.54). (Replacing solvent molecule) Placed Cl- in aa at (34.43, 14.06, -7.61). (Replacing solvent molecule) Placed Na+ in aa at (28.80, 13.85, -4.08). (Replacing solvent molecule) Placed Cl- in aa at (31.25, 10.88, -2.10). (Replacing solvent molecule) Placed Na+ in aa at (35.70, 7.27, -2.15). (Replacing solvent molecule) Placed Cl- in aa at (31.59, 5.90, -5.88). (Replacing solvent molecule) Placed Na+ in aa at (34.11, 3.84, -6.89). (Replacing solvent molecule) Placed Cl- in aa at (37.26, 5.03, -4.48). (Replacing solvent molecule) Placed Na+ in aa at (30.89, 16.74, -10.17). (Replacing solvent molecule) Placed Cl- in aa at (30.84, 18.42, -17.14). (Replacing solvent molecule) Placed Na+ in aa at (23.99, 19.07, -20.37). (Replacing solvent molecule) Placed Cl- in aa at (21.03, 20.89, -19.96). (Replacing solvent molecule) Placed Na+ in aa at (19.14, 22.85, -11.94). (Replacing solvent molecule) Placed Cl- in aa at (18.11, 26.42, -10.10). (Replacing solvent molecule) Placed Na+ in aa at (18.32, 20.70, -7.69). (Replacing solvent molecule) Placed Cl- in aa at (19.31, 25.31, -6.32). (Replacing solvent molecule) Placed Na+ in aa at (7.85, 28.23, -1.59). (Replacing solvent molecule) Placed Cl- in aa at (5.42, 24.57, -3.04). (No solvent overlap) Placed Na+ in aa at (8.23, 22.45, -4.77). (Replacing solvent molecule) Placed Cl- in aa at (22.92, 17.49, -25.64). 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: -38.77 -42.55 -41.77 45.05 40.02 43.05 sized: 89.23 85.45 86.23 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.70% of box, grid points 98482 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 130 sec (Replacing solvent molecule) Placed Na+ in aa at (29.97, 0.68, -27.37). (Replacing solvent molecule) Placed Cl- in aa at (23.80, -1.40, -39.30). (Replacing solvent molecule) Placed Na+ in aa at (23.33, 2.93, -36.22). (Replacing solvent molecule) Placed Cl- in aa at (28.97, 5.52, -30.02). (Replacing solvent molecule) Placed Na+ in aa at (31.47, 3.08, -31.36). (Replacing solvent molecule) Placed Cl- in aa at (29.16, -4.19, -27.90). (Replacing solvent molecule) Placed Na+ in aa at (31.03, -1.84, -29.76). (Replacing solvent molecule) Placed Cl- in aa at (32.55, -1.54, -32.34). (Replacing solvent molecule) Placed Na+ in aa at (27.26, 6.24, -27.50). (Replacing solvent molecule) Placed Cl- in aa at (31.35, 3.66, -28.06). (Replacing solvent molecule) Placed Na+ in aa at (27.96, -3.60, -40.27). (Replacing solvent molecule) Placed Cl- in aa at (26.08, 1.08, -37.14). (Replacing solvent molecule) Placed Na+ in aa at (33.14, -5.39, -26.16). (Replacing solvent molecule) Placed Cl- in aa at (32.41, -2.39, -26.27). (Replacing solvent molecule) Placed Na+ in aa at (32.19, -3.00, -22.04). (Replacing solvent molecule) Placed Cl- in aa at (37.17, -6.76, -20.32). (Replacing solvent molecule) Placed Na+ in aa at (34.89, -6.83, -16.98). (Replacing solvent molecule) Placed Cl- in aa at (34.67, -3.01, -19.18). (Replacing solvent molecule) Placed Na+ in aa at (26.49, -3.78, -34.83). (Replacing solvent molecule) Placed Cl- in aa at (29.98, -7.81, -38.49). 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: -38.77 -42.55 -48.06 45.05 40.02 43.05 sized: 89.23 85.45 79.94 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.85% of box, grid points 101714 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 109 sec (Replacing solvent molecule) Placed Na+ in aa at (21.93, 7.20, 19.12). (Replacing solvent molecule) Placed Cl- in aa at (11.46, -13.06, 13.67). (Replacing solvent molecule) Placed Na+ in aa at (14.24, -13.65, 13.55). (Replacing solvent molecule) Placed Cl- in aa at (16.99, -10.42, 15.79). (Replacing solvent molecule) Placed Na+ in aa at (16.63, -11.26, 19.71). (Replacing solvent molecule) Placed Cl- in aa at (8.92, -0.48, 26.59). (Replacing solvent molecule) Placed Na+ in aa at (12.29, -2.64, 27.15). (Replacing solvent molecule) Placed Cl- in aa at (-4.69, -24.49, -17.56). (Replacing solvent molecule) Placed Na+ in aa at (-2.59, -24.21, -19.53). (Replacing solvent molecule) Placed Cl- in aa at (14.78, -1.37, 25.55). (Replacing solvent molecule) Placed Na+ in aa at (12.08, 2.16, 27.46). (Replacing solvent molecule) Placed Cl- in aa at (9.95, 3.50, 29.72). (Replacing solvent molecule) Placed Na+ in aa at (4.51, 2.63, 31.33). (Replacing solvent molecule) Placed Cl- in aa at (1.01, 3.30, 28.78). (Replacing solvent molecule) Placed Na+ in aa at (6.15, -2.75, 29.07). (Replacing solvent molecule) Placed Cl- in aa at (3.47, -1.67, 32.01). (Replacing solvent molecule) Placed Na+ in aa at (0.19, -0.76, 29.39). (Replacing solvent molecule) Placed Cl- in aa at (2.94, -1.50, 27.87). (Replacing solvent molecule) Placed Na+ in aa at (4.67, -4.61, 25.01). (Replacing solvent molecule) Placed Cl- in aa at (7.64, -6.38, 27.75). 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: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -38.77 -42.55 -48.06 45.05 40.02 43.05 sized: 89.23 85.45 79.94 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.96% of box, grid points 104078 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 98 sec (Replacing solvent molecule) Placed Na+ in aa at (20.41, -4.45, -28.65). (Replacing solvent molecule) Placed Cl- in aa at (24.86, -8.06, -28.70). (Replacing solvent molecule) Placed Na+ in aa at (23.41, -10.34, -30.67). (Replacing solvent molecule) Placed Cl- in aa at (26.50, -10.41, -35.50). (Replacing solvent molecule) Placed Na+ in aa at (29.21, -13.60, -38.26). (Replacing solvent molecule) Placed Cl- in aa at (-7.58, 2.94, 3.84). (No solvent overlap) Placed Na+ in aa at (-8.77, -0.55, 2.94). (Replacing solvent molecule) Placed Cl- in aa at (6.57, -25.77, -18.88). (Replacing solvent molecule) Placed Na+ in aa at (7.98, -20.42, -20.57). (Replacing solvent molecule) Placed Cl- in aa at (18.71, -10.93, -23.16). (Replacing solvent molecule) Placed Na+ in aa at (16.16, -13.20, -19.77). (Replacing solvent molecule) Placed Cl- in aa at (8.82, -19.93, -17.84). (Replacing solvent molecule) Placed Na+ in aa at (9.35, -19.84, -13.18). (Replacing solvent molecule) Placed Cl- in aa at (12.08, -20.83, -12.36). (Replacing solvent molecule) Placed Na+ in aa at (12.99, -18.88, -14.79). (Replacing solvent molecule) Placed Cl- in aa at (15.03, -15.01, -17.08). (Replacing solvent molecule) Placed Na+ in aa at (19.24, -15.40, -20.67). (Replacing solvent molecule) Placed Cl- in aa at (16.02, -15.69, -21.80). (Replacing solvent molecule) Placed Na+ in aa at (9.71, -16.38, -23.06). (Replacing solvent molecule) Placed Cl- in aa at (8.30, -15.48, -25.22). Done adding ions. > > saveamberparm aa m4.topo m4.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 total 1507 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 CTHR 1 HEM 1 NHIE 1 WAT 18133 ) (no restraints) > > quit Quit log started: Thu Jul 17 11:09:54 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 HIE, term: Terminal/beginning, seq. number: 0 to: NHIE. (Residue 1: SER, Nonterminal, was not found in name map.) (Residue 2: HIE, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: LEU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: LYS, Nonterminal, was not found in name map.) (Residue 7: LYS, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: ILE, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: PRO, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: PRO, Nonterminal, was not found in name map.) (Residue 18: PHE, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLY, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: ILE, Nonterminal, was not found in name map.) (Residue 23: LEU, Nonterminal, was not found in name map.) (Residue 24: SER, Nonterminal, was not found in name map.) (Residue 25: TYR, Nonterminal, was not found in name map.) (Residue 26: HID, Nonterminal, was not found in name map.) (Residue 27: LYS, Nonterminal, was not found in name map.) (Residue 28: GLY, Nonterminal, was not found in name map.) (Residue 29: PHE, Nonterminal, was not found in name map.) (Residue 30: CYS, Nonterminal, was not found in name map.) (Residue 31: MET, Nonterminal, was not found in name map.) (Residue 32: PHE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: MET, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: CYS, Nonterminal, was not found in name map.) (Residue 37: HIE, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: TYR, Nonterminal, was not found in name map.) (Residue 41: GLY, Nonterminal, was not found in name map.) (Residue 42: LYS, Nonterminal, was not found in name map.) (Residue 43: VAL, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: GLY, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: TYR, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: GLN, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: ASP, Nonterminal, was not found in name map.) (Residue 59: PRO, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, Nonterminal, was not found in name map.) (Residue 62: ILE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: THR, Nonterminal, was not found in name map.) (Residue 65: VAL, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLU, Nonterminal, was not found in name map.) (Residue 70: CYS, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: SER, Nonterminal, was not found in name map.) (Residue 73: VAL, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: THR, Nonterminal, was not found in name map.) (Residue 76: ASN, Nonterminal, was not found in name map.) (Residue 77: ARG, Nonterminal, was not found in name map.) (Residue 78: ARG, Nonterminal, was not found in name map.) (Residue 79: PRO, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: PRO, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: PHE, Nonterminal, was not found in name map.) (Residue 86: MET, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: ALA, Nonterminal, was not found in name map.) (Residue 90: ILE, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ILE, Nonterminal, was not found in name map.) (Residue 93: ALA, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: ASP, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: GLU, Nonterminal, was not found in name map.) (Residue 98: TRP, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ARG, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: ARG, Nonterminal, was not found in name map.) (Residue 103: SER, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: LEU, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: THR, Nonterminal, was not found in name map.) (Residue 109: PHE, Nonterminal, was not found in name map.) (Residue 110: THR, Nonterminal, was not found in name map.) (Residue 111: SER, Nonterminal, was not found in name map.) (Residue 112: GLY, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLU, Nonterminal, was not found in name map.) (Residue 117: MET, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PRO, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: ALA, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: TYR, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ASP, Nonterminal, was not found in name map.) (Residue 127: VAL, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: VAL, Nonterminal, was not found in name map.) (Residue 130: ARG, Nonterminal, was not found in name map.) (Residue 131: ASN, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: ARG, Nonterminal, was not found in name map.) (Residue 134: ARG, Nonterminal, was not found in name map.) (Residue 135: GLU, Nonterminal, was not found in name map.) (Residue 136: ALA, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: THR, Nonterminal, was not found in name map.) (Residue 139: GLY, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: LEU, Nonterminal, was not found in name map.) (Residue 145: LYS, Nonterminal, was not found in name map.) (Residue 146: ASP, Nonterminal, was not found in name map.) (Residue 147: VAL, Nonterminal, was not found in name map.) (Residue 148: PHE, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: TYR, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: MET, Nonterminal, was not found in name map.) (Residue 154: ASP, Nonterminal, was not found in name map.) (Residue 155: VAL, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: SER, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: SER, Nonterminal, was not found in name map.) (Residue 161: PHE, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: VAL, Nonterminal, was not found in name map.) (Residue 164: ASN, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ASP, Nonterminal, was not found in name map.) (Residue 167: SER, Nonterminal, was not found in name map.) (Residue 168: LEU, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: PRO, Nonterminal, was not found in name map.) (Residue 172: GLN, Nonterminal, was not found in name map.) (Residue 173: ASP, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: PHE, Nonterminal, was not found in name map.) (Residue 176: VAL, Nonterminal, was not found in name map.) (Residue 177: GLU, Nonterminal, was not found in name map.) (Residue 178: ASN, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LYS, Nonterminal, was not found in name map.) (Residue 181: LYS, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: LEU, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: PHE, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: ASP, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: PHE, Nonterminal, was not found in name map.) (Residue 192: PHE, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: SER, Nonterminal, was not found in name map.) (Residue 195: ILE, Nonterminal, was not found in name map.) (Residue 196: THR, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: PHE, Nonterminal, was not found in name map.) (Residue 199: PRO, Nonterminal, was not found in name map.) (Residue 200: PHE, Nonterminal, was not found in name map.) (Residue 201: LEU, Nonterminal, was not found in name map.) (Residue 202: ILE, Nonterminal, was not found in name map.) (Residue 203: PRO, Nonterminal, was not found in name map.) (Residue 204: ILE, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: GLU, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: ASN, Nonterminal, was not found in name map.) (Residue 210: ILE, Nonterminal, was not found in name map.) (Residue 211: CYS, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: PHE, Nonterminal, was not found in name map.) (Residue 214: PRO, Nonterminal, was not found in name map.) (Residue 215: ARG, Nonterminal, was not found in name map.) (Residue 216: GLU, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: ASN, Nonterminal, was not found in name map.) (Residue 220: PHE, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: ARG, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: SER, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LYS, Nonterminal, was not found in name map.) (Residue 227: ARG, Nonterminal, was not found in name map.) (Residue 228: MET, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: ARG, Nonterminal, was not found in name map.) (Residue 233: LEU, Nonterminal, was not found in name map.) (Residue 234: GLU, Nonterminal, was not found in name map.) (Residue 235: ASP, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: GLN, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: HIE, Nonterminal, was not found in name map.) (Residue 240: ARG, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: ASP, Nonterminal, was not found in name map.) (Residue 243: PHE, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: GLN, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: MET, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ASP, Nonterminal, was not found in name map.) (Residue 250: SER, Nonterminal, was not found in name map.) (Residue 251: GLN, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: LYS, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: GLU, Nonterminal, was not found in name map.) (Residue 258: SER, Nonterminal, was not found in name map.) (Residue 259: HIE, Nonterminal, was not found in name map.) (Residue 260: LYS, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: LEU, Nonterminal, was not found in name map.) (Residue 263: SER, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: LEU, Nonterminal, was not found in name map.) (Residue 266: GLU, Nonterminal, was not found in name map.) (Residue 267: LEU, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ALA, Nonterminal, was not found in name map.) (Residue 270: GLN, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: ILE, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: PHE, Nonterminal, was not found in name map.) (Residue 275: ILE, Nonterminal, was not found in name map.) (Residue 276: PHE, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: TYR, Nonterminal, was not found in name map.) (Residue 280: GLU, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: THR, Nonterminal, was not found in name map.) (Residue 283: SER, Nonterminal, was not found in name map.) (Residue 284: SER, Nonterminal, was not found in name map.) (Residue 285: VAL, Nonterminal, was not found in name map.) (Residue 286: LEU, Nonterminal, was not found in name map.) (Residue 287: SER, Nonterminal, was not found in name map.) (Residue 288: PHE, Nonterminal, was not found in name map.) (Residue 289: ILE, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: TYR, Nonterminal, was not found in name map.) (Residue 292: GLU, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: ALA, Nonterminal, was not found in name map.) (Residue 295: THR, Nonterminal, was not found in name map.) (Residue 296: HIE, Nonterminal, was not found in name map.) (Residue 297: PRO, Nonterminal, was not found in name map.) (Residue 298: ASP, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: GLN, Nonterminal, was not found in name map.) (Residue 301: GLN, Nonterminal, was not found in name map.) (Residue 302: LYS, Nonterminal, was not found in name map.) (Residue 303: LEU, Nonterminal, was not found in name map.) (Residue 304: GLN, Nonterminal, was not found in name map.) (Residue 305: GLU, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ALA, Nonterminal, was not found in name map.) (Residue 310: VAL, Nonterminal, was not found in name map.) (Residue 311: LEU, Nonterminal, was not found in name map.) (Residue 312: PRO, Nonterminal, was not found in name map.) (Residue 313: ASN, Nonterminal, was not found in name map.) (Residue 314: LYS, Nonterminal, was not found in name map.) (Residue 315: ALA, Nonterminal, was not found in name map.) (Residue 316: PRO, Nonterminal, was not found in name map.) (Residue 317: PRO, Nonterminal, was not found in name map.) (Residue 318: THR, Nonterminal, was not found in name map.) (Residue 319: TYR, Nonterminal, was not found in name map.) (Residue 320: ASP, Nonterminal, was not found in name map.) (Residue 321: THR, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: MET, Nonterminal, was not found in name map.) (Residue 326: GLU, Nonterminal, was not found in name map.) (Residue 327: TYR, Nonterminal, was not found in name map.) (Residue 328: LEU, Nonterminal, was not found in name map.) (Residue 329: ASP, Nonterminal, was not found in name map.) (Residue 330: MET, Nonterminal, was not found in name map.) (Residue 331: VAL, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ASN, Nonterminal, was not found in name map.) (Residue 334: GLU, Nonterminal, was not found in name map.) (Residue 335: THR, Nonterminal, was not found in name map.) (Residue 336: LEU, Nonterminal, was not found in name map.) (Residue 337: ARG, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: PHE, Nonterminal, was not found in name map.) (Residue 340: PRO, Nonterminal, was not found in name map.) (Residue 341: ILE, Nonterminal, was not found in name map.) (Residue 342: ALA, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: ARG, Nonterminal, was not found in name map.) (Residue 345: LEU, Nonterminal, was not found in name map.) (Residue 346: GLU, Nonterminal, was not found in name map.) (Residue 347: ARG, Nonterminal, was not found in name map.) (Residue 348: VAL, Nonterminal, was not found in name map.) (Residue 349: CYS, Nonterminal, was not found in name map.) (Residue 350: LYS, Nonterminal, was not found in name map.) (Residue 351: LYS, Nonterminal, was not found in name map.) (Residue 352: ASP, Nonterminal, was not found in name map.) (Residue 353: VAL, Nonterminal, was not found in name map.) (Residue 354: GLU, Nonterminal, was not found in name map.) (Residue 355: ILE, Nonterminal, was not found in name map.) (Residue 356: ASN, Nonterminal, was not found in name map.) (Residue 357: GLY, Nonterminal, was not found in name map.) (Residue 358: MET, Nonterminal, was not found in name map.) (Residue 359: PHE, Nonterminal, was not found in name map.) (Residue 360: ILE, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: GLY, Nonterminal, was not found in name map.) (Residue 364: VAL, Nonterminal, was not found in name map.) (Residue 365: VAL, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: MET, Nonterminal, was not found in name map.) (Residue 368: ILE, Nonterminal, was not found in name map.) (Residue 369: PRO, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: TYR, Nonterminal, was not found in name map.) (Residue 372: ALA, Nonterminal, was not found in name map.) (Residue 373: LEU, Nonterminal, was not found in name map.) (Residue 374: HIE, Nonterminal, was not found in name map.) (Residue 375: ARG, Nonterminal, was not found in name map.) (Residue 376: ASP, Nonterminal, was not found in name map.) (Residue 377: PRO, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: TYR, Nonterminal, was not found in name map.) (Residue 380: TRP, Nonterminal, was not found in name map.) (Residue 381: THR, Nonterminal, was not found in name map.) (Residue 382: GLU, 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: LYS, 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: PRO, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: ARG, Nonterminal, was not found in name map.) (Residue 391: PHE, Nonterminal, was not found in name map.) (Residue 392: SER, Nonterminal, was not found in name map.) (Residue 393: LYS, Nonterminal, was not found in name map.) (Residue 394: LYS, Nonterminal, was not found in name map.) (Residue 395: ASN, Nonterminal, was not found in name map.) (Residue 396: LYS, Nonterminal, was not found in name map.) (Residue 397: ASP, Nonterminal, was not found in name map.) (Residue 398: ASN, Nonterminal, was not found in name map.) (Residue 399: ILE, Nonterminal, was not found in name map.) (Residue 400: ASP, Nonterminal, was not found in name map.) (Residue 401: PRO, Nonterminal, was not found in name map.) (Residue 402: TYR, Nonterminal, was not found in name map.) (Residue 403: ILE, Nonterminal, was not found in name map.) (Residue 404: TYR, Nonterminal, was not found in name map.) (Residue 405: THR, Nonterminal, was not found in name map.) (Residue 406: PRO, Nonterminal, was not found in name map.) (Residue 407: PHE, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: SER, Nonterminal, was not found in name map.) (Residue 410: GLY, Nonterminal, was not found in name map.) (Residue 411: PRO, Nonterminal, was not found in name map.) (Residue 412: ARG, Nonterminal, was not found in name map.) (Residue 413: ASN, Nonterminal, was not found in name map.) (Residue 414: CYP, Nonterminal, was not found in name map.) (Residue 415: ILE, Nonterminal, was not found in name map.) (Residue 416: GLY, Nonterminal, was not found in name map.) (Residue 417: MET, Nonterminal, was not found in name map.) (Residue 418: ARG, Nonterminal, was not found in name map.) (Residue 419: PHE, Nonterminal, was not found in name map.) (Residue 420: ALA, Nonterminal, was not found in name map.) (Residue 421: LEU, Nonterminal, was not found in name map.) (Residue 422: MET, Nonterminal, was not found in name map.) (Residue 423: ASN, Nonterminal, was not found in name map.) (Residue 424: MET, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: LEU, Nonterminal, was not found in name map.) (Residue 427: ALA, Nonterminal, was not found in name map.) (Residue 428: LEU, Nonterminal, was not found in name map.) (Residue 429: ILE, Nonterminal, was not found in name map.) (Residue 430: ARG, Nonterminal, was not found in name map.) (Residue 431: VAL, Nonterminal, was not found in name map.) (Residue 432: LEU, Nonterminal, was not found in name map.) (Residue 433: GLN, Nonterminal, was not found in name map.) (Residue 434: ASN, Nonterminal, was not found in name map.) (Residue 435: PHE, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: PHE, Nonterminal, was not found in name map.) (Residue 438: LYS, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: CYS, Nonterminal, was not found in name map.) (Residue 441: LYS, Nonterminal, was not found in name map.) (Residue 442: GLU, Nonterminal, was not found in name map.) (Residue 443: THR, Nonterminal, was not found in name map.) (Residue 444: GLN, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: PRO, Nonterminal, was not found in name map.) (Residue 447: LEU, Nonterminal, was not found in name map.) (Residue 448: LYS, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: SER, Nonterminal, was not found in name map.) (Residue 451: LEU, Nonterminal, was not found in name map.) (Residue 452: GLY, Nonterminal, was not found in name map.) (Residue 453: GLY, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: LEU, Nonterminal, was not found in name map.) (Residue 456: GLN, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: LYS, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: VAL, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: LEU, Nonterminal, was not found in name map.) (Residue 464: LYS, Nonterminal, was not found in name map.) (Residue 465: VAL, Nonterminal, was not found in name map.) (Residue 466: GLU, Nonterminal, was not found in name map.) (Residue 467: SER, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 471 to: CTHR. (Residue 472: HEM, Terminal/last, was not found in name map.) Joining NHIE - SER Joining SER - HIE Joining HIE - GLY Joining GLY - LEU Joining LEU - PHE Joining PHE - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - PRO Joining PRO - THR Joining THR - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - SER Joining SER - TYR Joining TYR - HID Joining HID - LYS Joining LYS - GLY Joining GLY - PHE Joining PHE - CYS Joining CYS - MET Joining MET - PHE Joining PHE - ASP Joining ASP - MET Joining MET - GLU Joining GLU - CYS Joining CYS - HIE Joining HIE - LYS Joining LYS - LYS Joining LYS - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - TRP Joining TRP - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - GLN Joining GLN - GLN Joining GLN - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ILE Joining ILE - THR Joining THR - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - MET Joining MET - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - CYS Joining CYS - TYR Joining TYR - SER Joining SER - VAL Joining VAL - PHE Joining PHE - THR Joining THR - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - PHE Joining PHE - MET Joining MET - LYS Joining LYS - SER Joining SER - ALA Joining ALA - ILE Joining ILE - SER Joining SER - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - TRP Joining TRP - LYS Joining LYS - ARG Joining ARG - LEU Joining LEU - ARG Joining ARG - SER Joining SER - LEU Joining LEU - LEU Joining LEU - SER Joining SER - PRO Joining PRO - THR Joining THR - PHE Joining PHE - THR Joining THR - SER Joining SER - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LYS Joining LYS - GLU Joining GLU - MET Joining MET - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - TYR Joining TYR - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ASN Joining ASN - LEU Joining LEU - ARG Joining ARG - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - GLU Joining GLU - THR Joining THR - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - THR Joining THR - LEU Joining LEU - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - TYR Joining TYR - SER Joining SER - MET Joining MET - ASP Joining ASP - VAL Joining VAL - ILE Joining ILE - THR Joining THR - SER Joining SER - THR Joining THR - SER Joining SER - PHE Joining PHE - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - SER Joining SER - LEU Joining LEU - ASN Joining ASN - ASN Joining ASN - PRO Joining PRO - GLN Joining GLN - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - VAL Joining VAL - GLU Joining GLU - ASN Joining ASN - THR Joining THR - LYS Joining LYS - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ARG Joining ARG - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - PHE Joining PHE - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ILE Joining ILE - THR Joining THR - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - ILE Joining ILE - CYS Joining CYS - VAL Joining VAL - PHE Joining PHE - PRO Joining PRO - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - ASN Joining ASN - PHE Joining PHE - LEU Joining LEU - ARG Joining ARG - LYS Joining LYS - SER Joining SER - VAL Joining VAL - LYS Joining LYS - ARG Joining ARG - MET Joining MET - LYS Joining LYS - GLU Joining GLU - SER Joining SER - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - THR Joining THR - GLN Joining GLN - LYS Joining LYS - HIE Joining HIE - ARG Joining ARG - VAL Joining VAL - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - MET Joining MET - ILE Joining ILE - ASP Joining ASP - SER Joining SER - GLN Joining GLN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLU Joining GLU - SER Joining SER - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - SER Joining SER - ILE Joining ILE - ILE Joining ILE - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - THR Joining THR - THR Joining THR - SER Joining SER - SER Joining SER - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ILE Joining ILE - MET Joining MET - TYR Joining TYR - GLU Joining GLU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - HIE Joining HIE - PRO Joining PRO - ASP Joining ASP - VAL Joining VAL - GLN Joining GLN - GLN Joining GLN - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - THR Joining THR - TYR Joining TYR - ASP Joining ASP - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - MET Joining MET - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - ASP Joining ASP - MET Joining MET - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - GLU Joining GLU - THR Joining THR - LEU Joining LEU - ARG Joining ARG - LEU Joining LEU - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - ALA Joining ALA - MET Joining MET - ARG Joining ARG - LEU Joining LEU - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - ILE Joining ILE - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PHE Joining PHE - ILE Joining ILE - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - MET Joining MET - ILE Joining ILE - PRO Joining PRO - SER Joining SER - TYR Joining TYR - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ARG Joining ARG - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - ARG Joining ARG - PHE Joining PHE - SER Joining SER - LYS Joining LYS - LYS Joining LYS - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - ILE Joining ILE - TYR Joining TYR - THR Joining THR - PRO Joining PRO - PHE Joining PHE - GLY Joining GLY - SER Joining SER - GLY Joining GLY - PRO Joining PRO - ARG Joining ARG - ASN Joining ASN - CYS Joining CYS - ILE Joining ILE - GLY Joining GLY - MET Joining MET - ARG Joining ARG - PHE Joining PHE - ALA Joining ALA - LEU Joining LEU - MET Joining MET - ASN Joining ASN - MET Joining MET - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - PHE Joining PHE - SER Joining SER - PHE Joining PHE - LYS Joining LYS - PRO Joining PRO - CYS Joining CYS - LYS Joining LYS - GLU Joining GLU - THR Joining THR - GLN Joining GLN - ILE Joining ILE - PRO Joining PRO - LEU Joining LEU - LYS Joining LYS - LEU Joining LEU - SER Joining SER - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - GLN Joining GLN - PRO Joining PRO - GLU Joining GLU - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - LYS Joining LYS - VAL Joining VAL - GLU Joining GLU - SER Joining SER - ARG Joining ARG - ASP Joining ASP - GLY Joining GLY - CTHR total atoms in file: 3844 Leap added 3910 missing atoms according to residue templates: 3880 H / lone pairs 30 unknown element > bond aa.415.SG aa.473.FE > > saveamberparm aa m5_invacuo.topo m5_invacuo.coords Checking Unit. WARNING: There is a bond of 4.012864 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: 3.000000 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.334738 to meet diagonal cut criterion Solute vdw bounding box: 47.609 77.279 63.687 Total bounding box for atom centers: 109.312 109.312 109.312 (box expansion for 'iso' is 56.7%) 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: 671183.333 A^3 (oct) Total mass 368894.968 amu, Density 0.913 g/cc Added 17443 residues. > > addions aa Cl- 0 3 Cl- ions required to neutralize. Adding 3 counter ions to "aa" using 1A grid Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.47 to 8.47 Box: enclosing: -40.26 -43.72 -40.55 40.18 40.36 41.11 sized: 87.74 84.28 87.45 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.10% of box, grid points 86000 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 114 sec (Replacing solvent molecule) Placed Cl- in aa at (-23.00, -15.18, -4.87). (Replacing solvent molecule) Placed Cl- in aa at (17.50, -10.27, 7.49). (Replacing solvent molecule) Placed Cl- in aa at (-13.73, -2.25, 24.78). 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: -39.58 -43.04 -39.87 39.50 39.68 40.43 sized: 88.42 84.96 88.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.48% of box, grid points 93974 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 86 sec (Replacing solvent molecule) Placed Na+ in aa at (-8.60, -26.37, -1.69). (Replacing solvent molecule) Placed Cl- in aa at (-23.35, -8.70, -2.58). (Replacing solvent molecule) Placed Na+ in aa at (-22.72, -8.41, 2.65). (Replacing solvent molecule) Placed Cl- in aa at (-21.38, -10.82, 2.66). (Replacing solvent molecule) Placed Na+ in aa at (-19.89, -21.01, 2.45). (Replacing solvent molecule) Placed Cl- in aa at (-19.90, -18.01, 7.10). (Replacing solvent molecule) Placed Na+ in aa at (-21.18, -18.61, 3.48). (Replacing solvent molecule) Placed Cl- in aa at (-19.17, -17.65, -0.87). (Replacing solvent molecule) Placed Na+ in aa at (-19.63, -13.03, 6.54). (Replacing solvent molecule) Placed Cl- in aa at (-16.19, -21.81, 5.99). (Replacing solvent molecule) Placed Na+ in aa at (-17.55, -15.58, 11.79). (Replacing solvent molecule) Placed Cl- in aa at (-19.94, -12.23, 16.71). (Replacing solvent molecule) Placed Na+ in aa at (-15.79, -11.09, 19.53). (Replacing solvent molecule) Placed Cl- in aa at (-17.40, -14.84, 9.30). (Replacing solvent molecule) Placed Na+ in aa at (-15.51, -19.73, 8.47). (Replacing solvent molecule) Placed Cl- in aa at (-24.18, -8.71, 6.84). (Replacing solvent molecule) Placed Na+ in aa at (30.07, 0.85, -27.55). (Replacing solvent molecule) Placed Cl- in aa at (18.06, -8.12, -22.34). (Replacing solvent molecule) Placed Na+ in aa at (21.71, -8.60, -22.96). (Replacing solvent molecule) Placed Cl- in aa at (29.25, -4.02, -28.08). 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: -39.58 -43.04 -39.87 39.50 39.68 40.43 sized: 88.42 84.96 88.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.54% of box, grid points 95145 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 87 sec (Replacing solvent molecule) Placed Na+ in aa at (27.15, 9.34, 14.27). (Replacing solvent molecule) Placed Cl- in aa at (31.87, 0.39, 8.57). (Replacing solvent molecule) Placed Na+ in aa at (36.08, -1.50, 5.28). (Replacing solvent molecule) Placed Cl- in aa at (-23.16, -21.52, 3.67). (Replacing solvent molecule) Placed Na+ in aa at (-22.88, -26.25, 5.61). (Replacing solvent molecule) Placed Cl- in aa at (-1.29, 32.95, 8.19). (Replacing solvent molecule) Placed Na+ in aa at (2.06, 32.98, 11.91). (Replacing solvent molecule) Placed Cl- in aa at (5.54, 33.52, 10.10). (Replacing solvent molecule) Placed Na+ in aa at (9.25, 33.92, 9.23). (Replacing solvent molecule) Placed Cl- in aa at (10.72, 29.35, 10.61). (Replacing solvent molecule) Placed Na+ in aa at (9.31, 32.24, 16.20). (Replacing solvent molecule) Placed Cl- in aa at (11.55, 33.10, 13.49). (Replacing solvent molecule) Placed Na+ in aa at (33.19, 3.03, 7.98). (Replacing solvent molecule) Placed Cl- in aa at (37.10, 5.26, 5.59). (Replacing solvent molecule) Placed Na+ in aa at (5.20, 30.63, 1.09). (Replacing solvent molecule) Placed Cl- in aa at (32.86, -0.29, 5.67). (Replacing solvent molecule) Placed Na+ in aa at (14.97, 30.40, 11.79). (Replacing solvent molecule) Placed Cl- in aa at (23.65, -10.25, 9.85). (Replacing solvent molecule) Placed Na+ in aa at (22.49, -7.62, 12.30). (Replacing solvent molecule) Placed Cl- in aa at (8.44, 29.09, 15.69). 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: -39.58 -43.04 -39.87 44.89 41.71 40.43 sized: 88.42 84.96 88.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.78% of box, grid points 100283 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 92 sec (No solvent overlap) Placed Na+ in aa at (4.42, 4.96, -22.87). (Replacing solvent molecule) Placed Cl- in aa at (7.36, 34.26, 2.99). (Replacing solvent molecule) Placed Na+ in aa at (2.40, 34.57, 6.00). (Replacing solvent molecule) Placed Cl- in aa at (0.30, 39.78, 13.59). (Replacing solvent molecule) Placed Na+ in aa at (2.51, 36.01, 12.41). (Replacing solvent molecule) Placed Cl- in aa at (2.46, 39.32, 9.39). (Replacing solvent molecule) Placed Na+ in aa at (-2.16, 41.04, 9.51). (Replacing solvent molecule) Placed Cl- in aa at (2.97, 30.02, 4.39). (Replacing solvent molecule) Placed Na+ in aa at (7.57, 28.54, 5.41). (Replacing solvent molecule) Placed Cl- in aa at (5.19, 33.38, 16.61). (Replacing solvent molecule) Placed Na+ in aa at (2.90, 29.40, 16.97). (Replacing solvent molecule) Placed Cl- in aa at (-0.08, 34.44, 13.95). (Replacing solvent molecule) Placed Na+ in aa at (3.33, 31.95, 2.59). (Replacing solvent molecule) Placed Cl- in aa at (1.33, 32.99, 0.73). (Replacing solvent molecule) Placed Na+ in aa at (1.54, 28.18, 0.42). (Replacing solvent molecule) Placed Cl- in aa at (5.25, 25.61, 2.51). (Replacing solvent molecule) Placed Na+ in aa at (6.37, 34.90, -0.62). (Replacing solvent molecule) Placed Cl- in aa at (4.44, 33.44, -2.20). (Replacing solvent molecule) Placed Na+ in aa at (1.06, 32.49, -2.92). (Replacing solvent molecule) Placed Cl- in aa at (-3.46, 32.27, -1.13). 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: -39.58 -43.04 -39.87 44.89 48.83 40.43 sized: 88.42 84.96 88.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.86% of box, grid points 101832 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 94 sec (Replacing solvent molecule) Placed Na+ in aa at (8.39, 16.18, 25.56). (Replacing solvent molecule) Placed Cl- in aa at (1.98, 28.07, -3.42). (Replacing solvent molecule) Placed Na+ in aa at (2.62, 31.30, -7.37). (Replacing solvent molecule) Placed Cl- in aa at (2.06, 32.98, -14.64). (Replacing solvent molecule) Placed Na+ in aa at (4.50, 33.69, -13.59). (Replacing solvent molecule) Placed Cl- in aa at (5.19, 33.38, -9.94). (Replacing solvent molecule) Placed Na+ in aa at (5.66, 29.47, -11.36). (Replacing solvent molecule) Placed Cl- in aa at (5.85, 30.52, -16.75). (Replacing solvent molecule) Placed Na+ in aa at (0.79, 28.80, -14.67). (Replacing solvent molecule) Placed Cl- in aa at (0.03, 29.72, -9.68). (Replacing solvent molecule) Placed Na+ in aa at (8.91, 26.23, -18.02). (Replacing solvent molecule) Placed Cl- in aa at (7.62, 24.90, -25.16). (Replacing solvent molecule) Placed Na+ in aa at (13.93, 23.34, -31.65). (Replacing solvent molecule) Placed Cl- in aa at (12.90, 25.31, -27.92). (Replacing solvent molecule) Placed Na+ in aa at (8.39, 30.68, -25.40). (Replacing solvent molecule) Placed Cl- in aa at (7.94, 28.40, -28.32). (Replacing solvent molecule) Placed Na+ in aa at (5.67, 21.74, -27.68). (Replacing solvent molecule) Placed Cl- in aa at (4.75, 17.62, -27.25). (Replacing solvent molecule) Placed Na+ in aa at (10.28, 28.72, -33.41). (Replacing solvent molecule) Placed Cl- in aa at (10.63, 25.23, -34.27). 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: -39.58 -43.04 -42.06 44.89 48.83 40.43 sized: 88.42 84.96 85.94 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.01% of box, grid points 105046 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 139 sec (Replacing solvent molecule) Placed Na+ in aa at (-0.02, -25.21, -13.17). (Replacing solvent molecule) Placed Cl- in aa at (-4.60, -24.32, -17.74). (No solvent overlap) Placed Na+ in aa at (-3.58, -24.04, -14.06). (Replacing solvent molecule) Placed Cl- in aa at (-1.39, -24.66, -16.66). (Replacing solvent molecule) Placed Na+ in aa at (-4.99, -30.80, -16.75). (Replacing solvent molecule) Placed Cl- in aa at (2.28, 25.57, -16.61). (Replacing solvent molecule) Placed Na+ in aa at (4.02, 23.87, -17.62). (Replacing solvent molecule) Placed Cl- in aa at (7.96, -25.83, -13.37). (Replacing solvent molecule) Placed Na+ in aa at (9.89, -27.40, -4.99). (Replacing solvent molecule) Placed Cl- in aa at (9.45, -32.33, -3.39). (Replacing solvent molecule) Placed Na+ in aa at (10.96, -34.07, -7.73). (Replacing solvent molecule) Placed Cl- in aa at (10.41, -29.48, -8.64). (Replacing solvent molecule) Placed Na+ in aa at (10.78, -26.62, -9.13). (Replacing solvent molecule) Placed Cl- in aa at (11.18, -23.35, -8.37). (Replacing solvent molecule) Placed Na+ in aa at (14.17, -21.71, -10.69). (Replacing solvent molecule) Placed Cl- in aa at (10.19, -30.27, -17.98). (Replacing solvent molecule) Placed Na+ in aa at (12.38, -25.47, -12.86). (Replacing solvent molecule) Placed Cl- in aa at (13.08, -18.71, -14.97). (Replacing solvent molecule) Placed Na+ in aa at (17.00, -19.73, -18.08). (Replacing solvent molecule) Placed Cl- in aa at (15.35, -27.33, -6.58). 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: -39.58 -43.04 -42.06 44.89 48.83 40.43 sized: 88.42 84.96 85.94 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.12% of box, grid points 107333 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 113 sec (Replacing solvent molecule) Placed Na+ in aa at (-17.84, -3.26, 15.13). (Replacing solvent molecule) Placed Cl- in aa at (-19.02, -6.14, 19.46). (Replacing solvent molecule) Placed Na+ in aa at (-17.08, -4.86, 17.88). (Replacing solvent molecule) Placed Cl- in aa at (-19.89, 1.98, 15.73). (Replacing solvent molecule) Placed Na+ in aa at (-21.12, 2.58, 19.34). (Replacing solvent molecule) Placed Cl- in aa at (-17.10, -2.41, 18.86). (Replacing solvent molecule) Placed Na+ in aa at (-14.88, -5.43, 20.39). (Replacing solvent molecule) Placed Cl- in aa at (-16.21, -5.98, 14.27). (Replacing solvent molecule) Placed Na+ in aa at (-18.22, -7.07, 12.14). (Replacing solvent molecule) Placed Cl- in aa at (-21.80, 6.35, 23.89). (Replacing solvent molecule) Placed Na+ in aa at (-19.47, 6.43, 26.90). (Replacing solvent molecule) Placed Cl- in aa at (-22.48, 3.67, 29.54). (Replacing solvent molecule) Placed Na+ in aa at (-24.08, 6.10, 28.97). (Replacing solvent molecule) Placed Cl- in aa at (14.88, -24.20, -14.46). (Replacing solvent molecule) Placed Na+ in aa at (18.05, -24.31, -17.54). (Replacing solvent molecule) Placed Cl- in aa at (19.52, -20.27, -17.04). (Replacing solvent molecule) Placed Na+ in aa at (19.73, -19.95, -12.74). (Replacing solvent molecule) Placed Cl- in aa at (18.78, -25.25, -15.04). (Replacing solvent molecule) Placed Na+ in aa at (17.27, -25.70, -12.67). (Replacing solvent molecule) Placed Cl- in aa at (16.86, -22.16, -9.06). 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: -39.58 -43.04 -42.06 44.89 48.83 40.43 sized: 88.42 84.96 85.94 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 5.17% of box, grid points 108480 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 103 sec (Replacing solvent molecule) Placed Na+ in aa at (13.93, -22.65, -5.10). (Replacing solvent molecule) Placed Cl- in aa at (7.22, -23.45, 4.22). (Replacing solvent molecule) Placed Na+ in aa at (5.67, -24.25, -1.13). (Replacing solvent molecule) Placed Cl- in aa at (11.63, -24.85, -1.40). (Replacing solvent molecule) Placed Na+ in aa at (13.74, -24.25, 3.70). (Replacing solvent molecule) Placed Cl- in aa at (-20.68, 7.87, 29.89). (Replacing solvent molecule) Placed Na+ in aa at (7.97, -26.09, 3.21). (Replacing solvent molecule) Placed Cl- in aa at (15.15, -21.91, 1.47). (Replacing solvent molecule) Placed Na+ in aa at (15.34, -19.96, -0.31). (Replacing solvent molecule) Placed Cl- in aa at (19.24, -21.45, 0.00). (Replacing solvent molecule) Placed Na+ in aa at (16.03, -20.27, 3.33). (Replacing solvent molecule) Placed Cl- in aa at (12.61, -18.01, 7.10). (Replacing solvent molecule) Placed Na+ in aa at (17.12, -25.66, -0.76). (Replacing solvent molecule) Placed Cl- in aa at (11.94, -27.19, 2.05). (Replacing solvent molecule) Placed Na+ in aa at (8.08, -15.91, 11.56). (Replacing solvent molecule) Placed Cl- in aa at (8.40, -13.78, 13.28). (Replacing solvent molecule) Placed Na+ in aa at (9.89, -4.41, 8.28). (Replacing solvent molecule) Placed Cl- in aa at (11.63, -1.86, 11.88). (Replacing solvent molecule) Placed Na+ in aa at (10.87, -0.94, 16.87). (Replacing solvent molecule) Placed Cl- in aa at (7.97, -3.09, 16.49). Done adding ions. > > saveamberparm aa m5.topo m5.coords Checking Unit. WARNING: There is a bond of 4.012864 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 total 1507 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 CTHR 1 HEM 1 NHIE 1 WAT 17302 ) (no restraints) > > quit Quit