log started: Fri Aug 15 13:24:35 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 > > gaffnew = loadamberparams Tmx_gaff.dat Loading parameters: ./Tmx_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) > frcmod = loadamberparams Tmx_f.frcmod Loading parameters: ./Tmx_f.frcmod Reading force field modification type file (frcmod) Reading title: REMARK 8/6 Modified Junmei frcmod Unknown keyword: REMARK ca- in parameter file. > OHT = loadmol2 FOHT_1_RED_ac.mol2 Loading Mol2 file: ./FOHT_1_RED_ac.mol2 Reading MOLECULE named OHT > > aa = loadpdb b22.pdb Loading PDB file: ./b22.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.) (Residue 473: OHT, 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: 3874 Leap added 3938 missing atoms according to residue templates: 3908 H / lone pairs 30 unknown element > > bond aa.415.SG aa.473.FE > > saveamberparm aa b22_invacuo.topo b22_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: 3.000400 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 1520 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 OHT 1 ) (no restraints) > > solvateoct aa TIP3PBOX 12.0 iso Scaling up box by a factor of 1.334807 to meet diagonal cut criterion Solute vdw bounding box: 47.632 77.216 63.618 Total bounding box for atom centers: 109.251 109.251 109.251 (box expansion for 'iso' is 56.6%) 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: 670069.369 A^3 (oct) Total mass 368255.558 amu, Density 0.913 g/cc Added 17386 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 39.96 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 86310 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 129 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 39.28 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.48% of box, grid points 94031 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 135 sec (Replacing solvent molecule) Placed Na+ in aa at (-12.54, -27.28, 0.20). (Replacing solvent molecule) Placed Cl- in aa at (-23.66, -8.64, -2.30). (Replacing solvent molecule) Placed Na+ in aa at (-6.70, -27.82, -1.93). (Replacing solvent molecule) Placed Cl- in aa at (31.57, 0.45, 8.84). (Replacing solvent molecule) Placed Na+ in aa at (35.78, -1.44, 5.56). (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 (9.15, -9.28, 10.17). (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). 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 43.57 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.60% of box, grid points 96484 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 138 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 (6.59, -24.03, -16.30). (Replacing solvent molecule) Placed Na+ in aa at (5.54, -22.28, -20.11). (Replacing solvent molecule) Placed Cl- in aa at (1.39, -18.93, -20.06). (Replacing solvent molecule) Placed Na+ in aa at (-5.60, -27.74, -16.17). (Replacing solvent molecule) Placed Cl- in aa at (-9.14, -24.04, -20.79). (No solvent overlap) Placed Na+ in aa at (-8.84, -20.00, -19.60). (Replacing solvent molecule) Placed Cl- in aa at (-10.80, -15.57, -20.61). (Replacing solvent molecule) Placed Na+ in aa at (-13.87, -19.75, -20.07). (Replacing solvent molecule) Placed Cl- in aa at (-15.82, -19.67, -17.80). (Replacing solvent molecule) Placed Na+ in aa at (-0.73, -21.76, -21.64). (Replacing solvent molecule) Placed Cl- in aa at (-4.19, -21.79, -21.61). (Replacing solvent molecule) Placed Na+ in aa at (-9.40, -19.84, -22.84). (Replacing solvent molecule) Placed Cl- in aa at (-13.29, -18.54, -23.99). (Replacing solvent molecule) Placed Na+ in aa at (-15.34, -17.44, -20.60). (Replacing solvent molecule) Placed Cl- in aa at (-4.90, -24.26, -17.46). (No solvent overlap) Placed Na+ in aa at (-7.84, -22.00, -15.60). (Replacing solvent molecule) Placed Cl- in aa at (1.86, -22.47, -19.80). 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 43.57 40.68 40.72 sized: 88.16 85.00 88.40 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.66% of box, grid points 97718 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 142 sec (Replacing solvent molecule) Placed Na+ in aa at (-0.32, -25.16, -12.89). (Replacing solvent molecule) Placed Cl- in aa at (6.59, -1.04, 23.53). (Replacing solvent molecule) Placed Na+ in aa at (2.04, -4.91, 22.79). (Replacing solvent molecule) Placed Cl- in aa at (5.11, -5.31, 20.16). (Replacing solvent molecule) Placed Na+ in aa at (6.46, -6.12, 24.24). (Replacing solvent molecule) Placed Cl- in aa at (3.19, -5.76, 26.92). (Replacing solvent molecule) Placed Na+ in aa at (7.66, -3.04, 16.76). (Replacing solvent molecule) Placed Cl- in aa at (10.57, -0.88, 17.15). (Replacing solvent molecule) Placed Na+ in aa at (8.91, -0.41, 11.62). (Replacing solvent molecule) Placed Cl- in aa at (11.33, -1.80, 12.16). (Replacing solvent molecule) Placed Na+ in aa at (16.82, -2.61, 12.79). (Replacing solvent molecule) Placed Cl- in aa at (21.26, -1.26, 10.89). (Replacing solvent molecule) Placed Na+ in aa at (24.87, 1.91, 13.64). (Replacing solvent molecule) Placed Cl- in aa at (27.62, 5.14, 15.89). (Replacing solvent molecule) Placed Na+ in aa at (29.76, 0.90, -27.27). (Replacing solvent molecule) Placed Cl- in aa at (28.95, -3.97, -27.80). (Replacing solvent molecule) Placed Na+ in aa at (30.07, -3.21, -23.99). (Replacing solvent molecule) Placed Cl- in aa at (15.37, -2.41, 8.89). (Replacing solvent molecule) Placed Na+ in aa at (32.34, -1.32, -32.24). (Replacing solvent molecule) Placed Cl- in aa at (31.60, 1.44, -29.20). Done adding ions. > addions aa Na+ 10 Cl- 10 Adding 20 counter ions to "aa" using 1A grid Total solute charge: 0.00 Max atom radius: 2.47 Grid extends from solute vdw + 1.32 to 7.79 Box: enclosing: -39.84 -43.00 -40.03 43.57 40.68 40.72 sized: 88.16 85.00 87.97 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.73% of box, grid points 99271 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 143 sec (Replacing solvent molecule) Placed Na+ in aa at (12.47, 13.18, 22.78). (Replacing solvent molecule) Placed Cl- in aa at (13.90, 16.80, 17.71). (Replacing solvent molecule) Placed Na+ in aa at (15.05, 18.71, 20.25). (Replacing solvent molecule) Placed Cl- in aa at (10.33, 25.29, 19.11). (No solvent overlap) Placed Na+ in aa at (8.16, 26.00, 15.97). (Replacing solvent molecule) Placed Cl- in aa at (9.01, 32.30, 16.48). (Replacing solvent molecule) Placed Na+ in aa at (10.46, 23.18, 22.69). (Replacing solvent molecule) Placed Cl- in aa at (9.59, 18.64, 21.84). (Replacing solvent molecule) Placed Na+ in aa at (8.09, 32.26, 13.56). (Replacing solvent molecule) Placed Cl- in aa at (12.75, 29.48, 13.90). (Replacing solvent molecule) Placed Na+ in aa at (18.16, 17.29, 14.94). (Replacing solvent molecule) Placed Cl- in aa at (18.61, 18.13, 19.36). (Replacing solvent molecule) Placed Na+ in aa at (10.99, 32.18, 10.99). (Replacing solvent molecule) Placed Cl- in aa at (5.55, 30.58, 10.08). (Replacing solvent molecule) Placed Na+ in aa at (1.76, 33.03, 12.18). (Replacing solvent molecule) Placed Cl- in aa at (-0.38, 34.49, 14.23). (Replacing solvent molecule) Placed Na+ in aa at (15.81, 7.53, 18.13). (Replacing solvent molecule) Placed Cl- in aa at (12.88, 10.42, 22.79). (Replacing solvent molecule) Placed Na+ in aa at (8.09, 16.23, 25.83). (Replacing solvent molecule) Placed Cl- in aa at (15.15, 5.78, 21.51). 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: -39.84 -43.00 -40.03 43.57 42.28 40.72 sized: 88.16 85.00 87.97 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.82% of box, grid points 101131 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 159 sec (No solvent overlap) Placed Na+ in aa at (10.16, 8.00, 20.97). (Replacing solvent molecule) Placed Cl- in aa at (-1.59, 33.01, 8.47). (Replacing solvent molecule) Placed Na+ in aa at (-3.93, 37.07, 9.29). (Replacing solvent molecule) Placed Cl- in aa at (9.15, 36.71, 10.17). (Replacing solvent molecule) Placed Na+ in aa at (7.27, 34.36, 12.03). (Replacing solvent molecule) Placed Cl- in aa at (4.01, 31.80, 15.03). (Replacing solvent molecule) Placed Na+ in aa at (2.32, 31.36, 19.46). (Replacing solvent molecule) Placed Cl- in aa at (-3.07, 33.46, 19.36). (Replacing solvent molecule) Placed Na+ in aa at (-4.71, 35.67, 14.16). (Replacing solvent molecule) Placed Cl- in aa at (-7.10, 37.18, 12.37). (Replacing solvent molecule) Placed Na+ in aa at (-1.75, 29.15, 21.21). (Replacing solvent molecule) Placed Cl- in aa at (1.67, 28.13, 23.41). (Replacing solvent molecule) Placed Na+ in aa at (3.71, 21.55, 29.44). (Replacing solvent molecule) Placed Cl- in aa at (6.74, 22.33, 28.00). (Replacing solvent molecule) Placed Na+ in aa at (7.17, 19.02, 26.56). (Replacing solvent molecule) Placed Cl- in aa at (2.99, 22.41, 27.01). (Replacing solvent molecule) Placed Na+ in aa at (0.59, 24.64, 24.38). (Replacing solvent molecule) Placed Cl- in aa at (8.50, 16.39, 28.57). (Replacing solvent molecule) Placed Na+ in aa at (10.52, 13.17, 26.93). (Replacing solvent molecule) Placed Cl- in aa at (13.99, 15.98, 25.70). 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 -40.03 43.57 44.97 40.72 sized: 88.16 85.00 87.97 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 1 sec Volume = 4.90% of box, grid points 102677 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 180 sec (No solvent overlap) Placed Na+ in aa at (18.16, -1.00, -30.03). (Replacing solvent molecule) Placed Cl- in aa at (16.03, 1.24, -33.55). (Replacing solvent molecule) Placed Na+ in aa at (13.67, 4.46, -36.91). (Replacing solvent molecule) Placed Cl- in aa at (36.81, -4.10, 4.31). (Replacing solvent molecule) Placed Na+ in aa at (36.71, -6.36, 2.79). (Replacing solvent molecule) Placed Cl- in aa at (31.63, -6.27, 5.98). (Replacing solvent molecule) Placed Na+ in aa at (31.98, -2.78, 4.61). (Replacing solvent molecule) Placed Cl- in aa at (32.50, -0.53, 2.94). (Replacing solvent molecule) Placed Na+ in aa at (31.14, 3.89, -1.41). (Replacing solvent molecule) Placed Cl- in aa at (31.26, 3.31, -4.71). (Replacing solvent molecule) Placed Na+ in aa at (33.90, 4.06, -6.79). (Replacing solvent molecule) Placed Cl- in aa at (30.93, 10.02, -4.81). (Replacing solvent molecule) Placed Na+ in aa at (34.28, 10.04, -1.09). (Replacing solvent molecule) Placed Cl- in aa at (35.31, 8.06, -4.82). (Replacing solvent molecule) Placed Na+ in aa at (34.62, 11.63, -7.00). (Replacing solvent molecule) Placed Cl- in aa at (31.41, 6.32, 1.09). (Replacing solvent molecule) Placed Na+ in aa at (33.32, -0.48, -1.65). (Replacing solvent molecule) Placed Cl- in aa at (35.67, 0.65, -0.85). (Replacing solvent molecule) Placed Na+ in aa at (35.63, 4.07, -0.86). (Replacing solvent molecule) Placed Cl- in aa at (32.93, -5.17, 0.49). 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: -39.84 -43.00 -44.70 44.60 44.97 40.72 sized: 88.16 85.00 83.30 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 2 sec Volume = 4.98% of box, grid points 104376 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 184 sec (Replacing solvent molecule) Placed Na+ in aa at (26.34, 15.49, -3.39). (Replacing solvent molecule) Placed Cl- in aa at (36.53, 8.80, 1.75). (Replacing solvent molecule) Placed Na+ in aa at (37.76, 10.59, -2.90). (Replacing solvent molecule) Placed Cl- in aa at (39.02, 14.06, -1.26). (Replacing solvent molecule) Placed Na+ in aa at (39.10, 14.53, 2.61). (Replacing solvent molecule) Placed Cl- in aa at (37.02, 11.86, -5.32). (Replacing solvent molecule) Placed Na+ in aa at (38.24, 8.56, -8.78). (Replacing solvent molecule) Placed Cl- in aa at (38.59, 11.96, -13.62). (Replacing solvent molecule) Placed Na+ in aa at (36.66, 10.50, -15.20). (Replacing solvent molecule) Placed Cl- in aa at (37.13, 5.14, -8.85). (Replacing solvent molecule) Placed Na+ in aa at (33.68, 2.71, -10.80). (Replacing solvent molecule) Placed Cl- in aa at (32.56, -0.24, -20.61). (Replacing solvent molecule) Placed Na+ in aa at (32.10, -2.81, -16.51). (Replacing solvent molecule) Placed Cl- in aa at (31.78, -0.07, -13.06). (Replacing solvent molecule) Placed Na+ in aa at (38.46, 14.06, -4.19). (Replacing solvent molecule) Placed Cl- in aa at (34.68, 16.39, -3.61). (Replacing solvent molecule) Placed Na+ in aa at (32.52, 16.85, 0.59). (Replacing solvent molecule) Placed Cl- in aa at (35.20, 15.33, 2.88). (Replacing solvent molecule) Placed Na+ in aa at (32.88, 3.09, -18.29). (Replacing solvent molecule) Placed Cl- in aa at (36.25, 6.52, -14.18). Done adding ions. > > saveamberparm aa b22.topo b22.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 1520 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 OHT 1 WAT 17248 ) (no restraints) > > quit Quit