log started: Wed Jun 23 15:19:19 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) 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" } >> { "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" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /net/bccs/cbu/linux64/amber11/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: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /net/bccs/cbu/linux64/amber11/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /net/bccs/cbu/linux64/amber11/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: /net/bccs/cbu/linux64/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /net/bccs/cbu/linux64/amber11/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. >> # >> loadOff all_aminoct03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminoct03.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS 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 >> loadOff all_aminont03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminont03.lib Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS 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 >> loadOff all_amino03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_amino03.lib Loading: ACE 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> >> # >> # 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" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > mol = loadpdb 2C7E_A.pdb_flsq.pdb Loading PDB file: ./2C7E_A.pdb_flsq.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: LYS, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: ASN, Nonterminal, was not found in name map.) (Residue 9: ASP, Nonterminal, was not found in name map.) (Residue 10: ALA, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: LYS, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: VAL, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ALA, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ALA, Nonterminal, was not found in name map.) (Residue 25: VAL, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: VAL, Nonterminal, was not found in name map.) (Residue 28: THR, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: PRO, Nonterminal, was not found in name map.) (Residue 32: LYS, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ARG, Nonterminal, was not found in name map.) (Residue 35: ASN, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: ASP, Nonterminal, was not found in name map.) (Residue 40: LYS, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: PHE, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: ALA, Nonterminal, was not found in name map.) (Residue 45: PRO, Nonterminal, was not found in name map.) (Residue 46: THR, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: LYS, Nonterminal, was not found in name map.) (Residue 50: ASP, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: VAL, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: VAL, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: GLU, Nonterminal, was not found in name map.) (Residue 58: ILE, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: ASP, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: GLU, Nonterminal, was not found in name map.) (Residue 66: ASN, Nonterminal, was not found in name map.) (Residue 67: MET, Nonterminal, was not found in name map.) (Residue 68: GLY, Nonterminal, was not found in name map.) (Residue 69: ALA, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: MET, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: LYS, Nonterminal, was not found in name map.) (Residue 74: GLU, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: ALA, Nonterminal, was not found in name map.) (Residue 77: SER, Nonterminal, was not found in name map.) (Residue 78: LYS, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: ASN, Nonterminal, was not found in name map.) (Residue 81: ASP, Nonterminal, was not found in name map.) (Residue 82: ALA, Nonterminal, was not found in name map.) (Residue 83: ALA, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: ASP, Nonterminal, was not found in name map.) (Residue 86: GLY, Nonterminal, was not found in name map.) (Residue 87: THR, Nonterminal, was not found in name map.) (Residue 88: THR, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: THR, Nonterminal, was not found in name map.) (Residue 92: VAL, Nonterminal, was not found in name map.) (Residue 93: LEU, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLN, Nonterminal, was not found in name map.) (Residue 96: ALA, Nonterminal, was not found in name map.) (Residue 97: ILE, Nonterminal, was not found in name map.) (Residue 98: ILE, Nonterminal, was not found in name map.) (Residue 99: THR, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: GLY, Nonterminal, was not found in name map.) (Residue 102: LEU, Nonterminal, was not found in name map.) (Residue 103: LYS, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: VAL, Nonterminal, was not found in name map.) (Residue 106: ALA, Nonterminal, was not found in name map.) (Residue 107: ALA, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: MET, Nonterminal, was not found in name map.) (Residue 110: ASN, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: MET, Nonterminal, was not found in name map.) (Residue 113: ASP, 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: ARG, Nonterminal, was not found in name map.) (Residue 117: GLY, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: ASP, Nonterminal, was not found in name map.) (Residue 120: LYS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: VAL, Nonterminal, was not found in name map.) (Residue 123: THR, Nonterminal, was not found in name map.) (Residue 124: VAL, Nonterminal, was not found in name map.) (Residue 125: ALA, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: GLU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: LYS, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: SER, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: CYS, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: SER, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: ALA, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: GLN, Nonterminal, was not found in name map.) (Residue 145: VAL, Nonterminal, was not found in name map.) (Residue 146: GLY, Nonterminal, was not found in name map.) (Residue 147: THR, Nonterminal, was not found in name map.) (Residue 148: ILE, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: ASN, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: GLU, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: VAL, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: LEU, Nonterminal, was not found in name map.) (Residue 160: ILE, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: MET, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: LYS, Nonterminal, was not found in name map.) (Residue 167: VAL, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: LYS, Nonterminal, was not found in name map.) (Residue 170: GLU, Nonterminal, was not found in name map.) (Residue 171: GLY, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: ILE, Nonterminal, was not found in name map.) (Residue 174: THR, Nonterminal, was not found in name map.) (Residue 175: VAL, Nonterminal, was not found in name map.) (Residue 176: GLU, Nonterminal, was not found in name map.) (Residue 177: ASP, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: GLY, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: GLN, Nonterminal, was not found in name map.) (Residue 183: ASP, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) (Residue 185: LEU, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: VAL, Nonterminal, was not found in name map.) (Residue 188: VAL, Nonterminal, was not found in name map.) (Residue 189: GLU, Nonterminal, was not found in name map.) (Residue 190: GLY, Nonterminal, was not found in name map.) (Residue 191: MET, Nonterminal, was not found in name map.) (Residue 192: GLN, Nonterminal, was not found in name map.) (Residue 193: PHE, Nonterminal, was not found in name map.) (Residue 194: ASP, Nonterminal, was not found in name map.) (Residue 195: ARG, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: TYR, Nonterminal, was not found in name map.) (Residue 198: LEU, Nonterminal, was not found in name map.) (Residue 199: SER, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: TYR, Nonterminal, was not found in name map.) (Residue 202: PHE, Nonterminal, was not found in name map.) (Residue 203: ILE, Nonterminal, was not found in name map.) (Residue 204: ASN, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: PRO, Nonterminal, was not found in name map.) (Residue 207: GLU, Nonterminal, was not found in name map.) (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: GLY, Nonterminal, was not found in name map.) (Residue 210: ALA, Nonterminal, was not found in name map.) (Residue 211: VAL, Nonterminal, was not found in name map.) (Residue 212: GLU, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: GLU, Nonterminal, was not found in name map.) (Residue 215: SER, Nonterminal, was not found in name map.) (Residue 216: PRO, Nonterminal, was not found in name map.) (Residue 217: PHE, Nonterminal, was not found in name map.) (Residue 218: ILE, Nonterminal, was not found in name map.) (Residue 219: LEU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: ASP, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: SER, Nonterminal, was not found in name map.) (Residue 227: ASN, Nonterminal, was not found in name map.) (Residue 228: ILE, Nonterminal, was not found in name map.) (Residue 229: ARG, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: MET, Nonterminal, was not found in name map.) (Residue 232: LEU, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: LEU, Nonterminal, was not found in name map.) (Residue 236: GLU, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: VAL, Nonterminal, was not found in name map.) (Residue 239: ALA, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: GLY, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: PRO, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: ILE, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ALA, Nonterminal, was not found in name map.) (Residue 250: GLU, Nonterminal, was not found in name map.) (Residue 251: ASP, Nonterminal, was not found in name map.) (Residue 252: VAL, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: GLY, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: ALA, Nonterminal, was not found in name map.) (Residue 257: LEU, Nonterminal, was not found in name map.) (Residue 258: ALA, Nonterminal, was not found in name map.) (Residue 259: THR, Nonterminal, was not found in name map.) (Residue 260: LEU, Nonterminal, was not found in name map.) (Residue 261: VAL, Nonterminal, was not found in name map.) (Residue 262: VAL, Nonterminal, was not found in name map.) (Residue 263: ASN, Nonterminal, was not found in name map.) (Residue 264: THR, Nonterminal, was not found in name map.) (Residue 265: MET, Nonterminal, was not found in name map.) (Residue 266: ARG, Nonterminal, was not found in name map.) (Residue 267: GLY, Nonterminal, was not found in name map.) (Residue 268: ILE, Nonterminal, was not found in name map.) (Residue 269: VAL, Nonterminal, was not found in name map.) (Residue 270: LYS, Nonterminal, was not found in name map.) (Residue 271: VAL, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: ALA, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: LYS, Nonterminal, was not found in name map.) (Residue 276: ALA, Nonterminal, was not found in name map.) (Residue 277: PRO, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: PHE, Nonterminal, was not found in name map.) (Residue 280: GLY, Nonterminal, was not found in name map.) (Residue 281: ASP, Nonterminal, was not found in name map.) (Residue 282: ARG, Nonterminal, was not found in name map.) (Residue 283: ARG, Nonterminal, was not found in name map.) (Residue 284: LYS, Nonterminal, was not found in name map.) (Residue 285: ALA, Nonterminal, was not found in name map.) (Residue 286: MET, Nonterminal, was not found in name map.) (Residue 287: LEU, Nonterminal, was not found in name map.) (Residue 288: GLN, Nonterminal, was not found in name map.) (Residue 289: ASP, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: ALA, Nonterminal, was not found in name map.) (Residue 292: THR, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: THR, Nonterminal, was not found in name map.) (Residue 295: GLY, Nonterminal, was not found in name map.) (Residue 296: GLY, Nonterminal, was not found in name map.) (Residue 297: THR, Nonterminal, was not found in name map.) (Residue 298: VAL, Nonterminal, was not found in name map.) (Residue 299: ILE, Nonterminal, was not found in name map.) (Residue 300: SER, Nonterminal, was not found in name map.) (Residue 301: GLU, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: ILE, Nonterminal, was not found in name map.) (Residue 304: GLY, Nonterminal, was not found in name map.) (Residue 305: MET, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: LEU, Nonterminal, was not found in name map.) (Residue 308: GLU, Nonterminal, was not found in name map.) (Residue 309: LYS, Nonterminal, was not found in name map.) (Residue 310: ALA, Nonterminal, was not found in name map.) (Residue 311: THR, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: ASP, Nonterminal, was not found in name map.) (Residue 315: LEU, Nonterminal, was not found in name map.) (Residue 316: GLY, Nonterminal, was not found in name map.) (Residue 317: GLN, Nonterminal, was not found in name map.) (Residue 318: ALA, Nonterminal, was not found in name map.) (Residue 319: LYS, Nonterminal, was not found in name map.) (Residue 320: ARG, Nonterminal, was not found in name map.) (Residue 321: VAL, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: ILE, Nonterminal, was not found in name map.) (Residue 324: ASN, Nonterminal, was not found in name map.) (Residue 325: LYS, Nonterminal, was not found in name map.) (Residue 326: ASP, Nonterminal, was not found in name map.) (Residue 327: THR, Nonterminal, was not found in name map.) (Residue 328: THR, Nonterminal, was not found in name map.) (Residue 329: THR, Nonterminal, was not found in name map.) (Residue 330: ILE, Nonterminal, was not found in name map.) (Residue 331: ILE, Nonterminal, was not found in name map.) (Residue 332: ASP, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: VAL, Nonterminal, was not found in name map.) (Residue 335: GLY, Nonterminal, was not found in name map.) (Residue 336: GLU, Nonterminal, was not found in name map.) (Residue 337: GLU, Nonterminal, was not found in name map.) (Residue 338: ALA, Nonterminal, was not found in name map.) (Residue 339: ALA, Nonterminal, was not found in name map.) (Residue 340: ILE, Nonterminal, was not found in name map.) (Residue 341: GLN, Nonterminal, was not found in name map.) (Residue 342: GLY, Nonterminal, was not found in name map.) (Residue 343: ARG, Nonterminal, was not found in name map.) (Residue 344: VAL, Nonterminal, was not found in name map.) (Residue 345: ALA, Nonterminal, was not found in name map.) (Residue 346: GLN, Nonterminal, was not found in name map.) (Residue 347: ILE, Nonterminal, was not found in name map.) (Residue 348: ARG, Nonterminal, was not found in name map.) (Residue 349: GLN, Nonterminal, was not found in name map.) (Residue 350: GLN, Nonterminal, was not found in name map.) (Residue 351: ILE, Nonterminal, was not found in name map.) (Residue 352: GLU, Nonterminal, was not found in name map.) (Residue 353: GLU, Nonterminal, was not found in name map.) (Residue 354: ALA, Nonterminal, was not found in name map.) (Residue 355: THR, Nonterminal, was not found in name map.) (Residue 356: SER, Nonterminal, was not found in name map.) (Residue 357: ASP, Nonterminal, was not found in name map.) (Residue 358: TYR, Nonterminal, was not found in name map.) (Residue 359: ASP, Nonterminal, was not found in name map.) (Residue 360: ARG, Nonterminal, was not found in name map.) (Residue 361: GLU, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: LEU, Nonterminal, was not found in name map.) (Residue 364: GLN, Nonterminal, was not found in name map.) (Residue 365: GLU, Nonterminal, was not found in name map.) (Residue 366: ARG, Nonterminal, was not found in name map.) (Residue 367: VAL, Nonterminal, was not found in name map.) (Residue 368: ALA, Nonterminal, was not found in name map.) (Residue 369: LYS, Nonterminal, was not found in name map.) (Residue 370: LEU, Nonterminal, was not found in name map.) (Residue 371: ALA, Nonterminal, was not found in name map.) (Residue 372: GLY, Nonterminal, was not found in name map.) (Residue 373: GLY, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: ALA, Nonterminal, was not found in name map.) (Residue 376: VAL, Nonterminal, was not found in name map.) (Residue 377: ILE, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: VAL, Nonterminal, was not found in name map.) (Residue 380: GLY, Nonterminal, was not found in name map.) (Residue 381: ALA, Nonterminal, was not found in name map.) (Residue 382: ALA, Nonterminal, was not found in name map.) (Residue 383: THR, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: VAL, Nonterminal, was not found in name map.) (Residue 386: GLU, Nonterminal, was not found in name map.) (Residue 387: MET, Nonterminal, was not found in name map.) (Residue 388: LYS, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: LYS, Nonterminal, was not found in name map.) (Residue 391: LYS, Nonterminal, was not found in name map.) (Residue 392: ALA, Nonterminal, was not found in name map.) (Residue 393: ARG, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: GLU, Nonterminal, was not found in name map.) (Residue 396: ASP, Nonterminal, was not found in name map.) (Residue 397: ALA, Nonterminal, was not found in name map.) (Residue 398: LEU, Nonterminal, was not found in name map.) (Residue 399: HID, Nonterminal, was not found in name map.) (Residue 400: ALA, Nonterminal, was not found in name map.) (Residue 401: THR, Nonterminal, was not found in name map.) (Residue 402: ARG, Nonterminal, was not found in name map.) (Residue 403: ALA, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: VAL, Nonterminal, was not found in name map.) (Residue 406: GLU, Nonterminal, was not found in name map.) (Residue 407: GLU, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: VAL, Nonterminal, was not found in name map.) (Residue 410: VAL, Nonterminal, was not found in name map.) (Residue 411: ALA, Nonterminal, was not found in name map.) (Residue 412: GLY, Nonterminal, was not found in name map.) (Residue 413: GLY, Nonterminal, was not found in name map.) (Residue 414: GLY, Nonterminal, was not found in name map.) (Residue 415: VAL, Nonterminal, was not found in name map.) (Residue 416: ALA, Nonterminal, was not found in name map.) (Residue 417: LEU, Nonterminal, was not found in name map.) (Residue 418: ILE, Nonterminal, was not found in name map.) (Residue 419: ARG, Nonterminal, was not found in name map.) (Residue 420: VAL, Nonterminal, was not found in name map.) (Residue 421: ALA, Nonterminal, was not found in name map.) (Residue 422: SER, Nonterminal, was not found in name map.) (Residue 423: LYS, Nonterminal, was not found in name map.) (Residue 424: LEU, Nonterminal, was not found in name map.) (Residue 425: ALA, Nonterminal, was not found in name map.) (Residue 426: ASP, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: ARG, Nonterminal, was not found in name map.) (Residue 429: GLY, Nonterminal, was not found in name map.) (Residue 430: GLN, Nonterminal, was not found in name map.) (Residue 431: ASN, Nonterminal, was not found in name map.) (Residue 432: GLU, Nonterminal, was not found in name map.) (Residue 433: ASP, Nonterminal, was not found in name map.) (Residue 434: GLN, Nonterminal, was not found in name map.) (Residue 435: ASN, Nonterminal, was not found in name map.) (Residue 436: VAL, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: ILE, Nonterminal, was not found in name map.) (Residue 439: LYS, Nonterminal, was not found in name map.) (Residue 440: VAL, Nonterminal, was not found in name map.) (Residue 441: ALA, Nonterminal, was not found in name map.) (Residue 442: LEU, Nonterminal, was not found in name map.) (Residue 443: ARG, Nonterminal, was not found in name map.) (Residue 444: ALA, Nonterminal, was not found in name map.) (Residue 445: MET, Nonterminal, was not found in name map.) (Residue 446: GLU, Nonterminal, was not found in name map.) (Residue 447: ALA, Nonterminal, was not found in name map.) (Residue 448: PRO, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: ARG, Nonterminal, was not found in name map.) (Residue 451: GLN, Nonterminal, was not found in name map.) (Residue 452: ILE, Nonterminal, was not found in name map.) (Residue 453: VAL, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: ASN, Nonterminal, was not found in name map.) (Residue 456: CYS, Nonterminal, was not found in name map.) (Residue 457: GLY, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: GLU, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: SER, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: VAL, Nonterminal, was not found in name map.) (Residue 464: ALA, Nonterminal, was not found in name map.) (Residue 465: ASN, Nonterminal, was not found in name map.) (Residue 466: THR, Nonterminal, was not found in name map.) (Residue 467: VAL, Nonterminal, was not found in name map.) (Residue 468: LYS, Nonterminal, was not found in name map.) (Residue 469: GLY, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) (Residue 471: ASP, Nonterminal, was not found in name map.) (Residue 472: GLY, Nonterminal, was not found in name map.) (Residue 473: ASN, Nonterminal, was not found in name map.) (Residue 474: TYR, Nonterminal, was not found in name map.) (Residue 475: GLY, Nonterminal, was not found in name map.) (Residue 476: TYR, Nonterminal, was not found in name map.) (Residue 477: ASN, Nonterminal, was not found in name map.) (Residue 478: ALA, Nonterminal, was not found in name map.) (Residue 479: ALA, Nonterminal, was not found in name map.) (Residue 480: THR, Nonterminal, was not found in name map.) (Residue 481: GLU, Nonterminal, was not found in name map.) (Residue 482: GLU, Nonterminal, was not found in name map.) (Residue 483: TYR, Nonterminal, was not found in name map.) (Residue 484: GLY, Nonterminal, was not found in name map.) (Residue 485: ASN, Nonterminal, was not found in name map.) (Residue 486: MET, Nonterminal, was not found in name map.) (Residue 487: ILE, Nonterminal, was not found in name map.) (Residue 488: ASP, Nonterminal, was not found in name map.) (Residue 489: MET, Nonterminal, was not found in name map.) (Residue 490: GLY, Nonterminal, was not found in name map.) (Residue 491: ILE, Nonterminal, was not found in name map.) (Residue 492: LEU, Nonterminal, was not found in name map.) (Residue 493: ASP, Nonterminal, was not found in name map.) (Residue 494: PRO, Nonterminal, was not found in name map.) (Residue 495: THR, Nonterminal, was not found in name map.) (Residue 496: LYS, Nonterminal, was not found in name map.) (Residue 497: VAL, Nonterminal, was not found in name map.) (Residue 498: THR, Nonterminal, was not found in name map.) (Residue 499: ARG, Nonterminal, was not found in name map.) (Residue 500: SER, Nonterminal, was not found in name map.) (Residue 501: ALA, Nonterminal, was not found in name map.) (Residue 502: LEU, Nonterminal, was not found in name map.) (Residue 503: GLN, Nonterminal, was not found in name map.) (Residue 504: TYR, Nonterminal, was not found in name map.) (Residue 505: ALA, Nonterminal, was not found in name map.) (Residue 506: ALA, Nonterminal, was not found in name map.) (Residue 507: SER, Nonterminal, was not found in name map.) (Residue 508: VAL, Nonterminal, was not found in name map.) (Residue 509: ALA, Nonterminal, was not found in name map.) (Residue 510: GLY, Nonterminal, was not found in name map.) (Residue 511: LEU, Nonterminal, was not found in name map.) (Residue 512: MET, Nonterminal, was not found in name map.) (Residue 513: ILE, Nonterminal, was not found in name map.) (Residue 514: THR, Nonterminal, was not found in name map.) (Residue 515: THR, Nonterminal, was not found in name map.) (Residue 516: GLU, Nonterminal, was not found in name map.) (Residue 517: CYS, Nonterminal, was not found in name map.) (Residue 518: MET, Nonterminal, was not found in name map.) (Residue 519: VAL, Nonterminal, was not found in name map.) (Residue 520: THR, Nonterminal, was not found in name map.) (Residue 521: ASP, Nonterminal, was not found in name map.) (Residue 522: LEU, Nonterminal, was not found in name map.) Mapped residue PRO, term: Terminal/last, seq. number: 523 to: CPRO. Joining NALA - ALA Joining ALA - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - GLY Joining GLY - VAL Joining VAL - LYS Joining LYS - MET Joining MET - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - THR Joining THR - LEU Joining LEU - GLY Joining GLY - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - PRO Joining PRO - THR Joining THR - ILE Joining ILE - THR Joining THR - LYS Joining LYS - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - SER Joining SER - VAL Joining VAL - ALA Joining ALA - ARG Joining ARG - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LYS Joining LYS - PHE Joining PHE - GLU Joining GLU - ASN Joining ASN - MET Joining MET - GLY Joining GLY - ALA Joining ALA - GLN Joining GLN - MET Joining MET - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - THR Joining THR - THR Joining THR - THR Joining THR - ALA Joining ALA - THR Joining THR - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - ALA Joining ALA - ILE Joining ILE - ILE Joining ILE - THR Joining THR - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - MET Joining MET - ASN Joining ASN - PRO Joining PRO - MET Joining MET - ASP Joining ASP - LEU Joining LEU - LYS Joining LYS - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - THR Joining THR - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - VAL Joining VAL - PRO Joining PRO - CYS Joining CYS - SER Joining SER - ASP Joining ASP - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - GLY Joining GLY - THR Joining THR - ILE Joining ILE - SER Joining SER - ALA Joining ALA - ASN Joining ASN - SER Joining SER - ASP Joining ASP - GLU Joining GLU - THR Joining THR - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - MET Joining MET - ASP Joining ASP - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - THR Joining THR - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - GLY Joining GLY - THR Joining THR - GLY Joining GLY - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - MET Joining MET - GLN Joining GLN - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - PRO Joining PRO - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - THR Joining THR - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - SER Joining SER - PRO Joining PRO - PHE Joining PHE - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LYS Joining LYS - LYS Joining LYS - ILE Joining ILE - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ARG Joining ARG - GLU Joining GLU - MET Joining MET - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - THR Joining THR - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - THR Joining THR - MET Joining MET - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ARG Joining ARG - ARG Joining ARG - LYS Joining LYS - ALA Joining ALA - MET Joining MET - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - ALA Joining ALA - THR Joining THR - LEU Joining LEU - THR Joining THR - GLY Joining GLY - GLY Joining GLY - THR Joining THR - VAL Joining VAL - ILE Joining ILE - SER Joining SER - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - GLY Joining GLY - MET Joining MET - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLY Joining GLY - GLN Joining GLN - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - THR Joining THR - THR Joining THR - THR Joining THR - ILE Joining ILE - ILE Joining ILE - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - ILE Joining ILE - GLN Joining GLN - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - ILE Joining ILE - ARG Joining ARG - GLN Joining GLN - GLN Joining GLN - ILE Joining ILE - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - THR Joining THR - SER Joining SER - ASP Joining ASP - TYR Joining TYR - ASP Joining ASP - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - VAL Joining VAL - GLU Joining GLU - MET Joining MET - LYS Joining LYS - GLU Joining GLU - LYS Joining LYS - LYS Joining LYS - ALA Joining ALA - ARG Joining ARG - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ALA Joining ALA - THR Joining THR - ARG Joining ARG - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - GLN Joining GLN - ASN Joining ASN - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Joining ASP - GLN Joining GLN - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - ALA Joining ALA - MET Joining MET - GLU Joining GLU - ALA Joining ALA - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - GLN Joining GLN - ILE Joining ILE - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - TYR Joining TYR - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - GLU Joining GLU - TYR Joining TYR - GLY Joining GLY - ASN Joining ASN - MET Joining MET - ILE Joining ILE - ASP Joining ASP - MET Joining MET - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - THR Joining THR - LYS Joining LYS - VAL Joining VAL - THR Joining THR - ARG Joining ARG - SER Joining SER - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - TYR Joining TYR - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - LEU Joining LEU - MET Joining MET - ILE Joining ILE - THR Joining THR - THR Joining THR - GLU Joining GLU - CYS Joining CYS - MET Joining MET - VAL Joining VAL - THR Joining THR - ASP Joining ASP - LEU Joining LEU - CPRO Added missing heavy atom: .R.A total atoms in file: 3846 Leap added 3978 missing atoms according to residue templates: 5 Heavy 3973 H / lone pairs > > #w = loadpdb waters_with_hbond_after_min_sol.pdb > #mol = combine {mol w} > > saveamberparm mol 2C7E_chainA_noWAT.prmtop 2C7E_chainA_noWAT.inpcrd Checking Unit. WARNING: There is a bond of 4.940917 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 8.152534 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -19.000003 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. total 1366 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 CPRO 1 NALA 1 ) (no restraints) > > #solvateoct mol TIP3PBOX 16.0 0.78 > #saveamberparm mol 2C7E_chainA_sol.prmtop 2C7E_chainA_sol.inpcrd > quit Quit log started: Wed Jun 23 15:23:01 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) 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" } >> { "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" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /net/bccs/cbu/linux64/amber11/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: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /net/bccs/cbu/linux64/amber11/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /net/bccs/cbu/linux64/amber11/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: /net/bccs/cbu/linux64/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /net/bccs/cbu/linux64/amber11/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. >> # >> loadOff all_aminoct03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminoct03.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS 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 >> loadOff all_aminont03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminont03.lib Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS 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 >> loadOff all_amino03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_amino03.lib Loading: ACE 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> >> # >> # 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" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > mol = loadpdb 2C7E_A.pdb_flsq.pdb Loading PDB file: ./2C7E_A.pdb_flsq.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: LYS, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: ASN, Nonterminal, was not found in name map.) (Residue 9: ASP, Nonterminal, was not found in name map.) (Residue 10: ALA, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: LYS, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: VAL, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ALA, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ALA, Nonterminal, was not found in name map.) (Residue 25: VAL, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: VAL, Nonterminal, was not found in name map.) (Residue 28: THR, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: PRO, Nonterminal, was not found in name map.) (Residue 32: LYS, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ARG, Nonterminal, was not found in name map.) (Residue 35: ASN, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: ASP, Nonterminal, was not found in name map.) (Residue 40: LYS, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: PHE, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: ALA, Nonterminal, was not found in name map.) (Residue 45: PRO, Nonterminal, was not found in name map.) (Residue 46: THR, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: LYS, Nonterminal, was not found in name map.) (Residue 50: ASP, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: VAL, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: VAL, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: GLU, Nonterminal, was not found in name map.) (Residue 58: ILE, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: ASP, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: GLU, Nonterminal, was not found in name map.) (Residue 66: ASN, Nonterminal, was not found in name map.) (Residue 67: MET, Nonterminal, was not found in name map.) (Residue 68: GLY, Nonterminal, was not found in name map.) (Residue 69: ALA, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: MET, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: LYS, Nonterminal, was not found in name map.) (Residue 74: GLU, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: ALA, Nonterminal, was not found in name map.) (Residue 77: SER, Nonterminal, was not found in name map.) (Residue 78: LYS, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: ASN, Nonterminal, was not found in name map.) (Residue 81: ASP, Nonterminal, was not found in name map.) (Residue 82: ALA, Nonterminal, was not found in name map.) (Residue 83: ALA, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: ASP, Nonterminal, was not found in name map.) (Residue 86: GLY, Nonterminal, was not found in name map.) (Residue 87: THR, Nonterminal, was not found in name map.) (Residue 88: THR, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: THR, Nonterminal, was not found in name map.) (Residue 92: VAL, Nonterminal, was not found in name map.) (Residue 93: LEU, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLN, Nonterminal, was not found in name map.) (Residue 96: ALA, Nonterminal, was not found in name map.) (Residue 97: ILE, Nonterminal, was not found in name map.) (Residue 98: ILE, Nonterminal, was not found in name map.) (Residue 99: THR, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: GLY, Nonterminal, was not found in name map.) (Residue 102: LEU, Nonterminal, was not found in name map.) (Residue 103: LYS, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: VAL, Nonterminal, was not found in name map.) (Residue 106: ALA, Nonterminal, was not found in name map.) (Residue 107: ALA, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: MET, Nonterminal, was not found in name map.) (Residue 110: ASN, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: MET, Nonterminal, was not found in name map.) (Residue 113: ASP, 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: ARG, Nonterminal, was not found in name map.) (Residue 117: GLY, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: ASP, Nonterminal, was not found in name map.) (Residue 120: LYS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: VAL, Nonterminal, was not found in name map.) (Residue 123: THR, Nonterminal, was not found in name map.) (Residue 124: VAL, Nonterminal, was not found in name map.) (Residue 125: ALA, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: GLU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: LYS, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: SER, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: CYS, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: SER, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: ALA, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: GLN, Nonterminal, was not found in name map.) (Residue 145: VAL, Nonterminal, was not found in name map.) (Residue 146: GLY, Nonterminal, was not found in name map.) (Residue 147: THR, Nonterminal, was not found in name map.) (Residue 148: ILE, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: ASN, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: GLU, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: VAL, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: LEU, Nonterminal, was not found in name map.) (Residue 160: ILE, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: MET, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: LYS, Nonterminal, was not found in name map.) (Residue 167: VAL, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: LYS, Nonterminal, was not found in name map.) (Residue 170: GLU, Nonterminal, was not found in name map.) (Residue 171: GLY, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: ILE, Nonterminal, was not found in name map.) (Residue 174: THR, Nonterminal, was not found in name map.) (Residue 175: VAL, Nonterminal, was not found in name map.) (Residue 176: GLU, Nonterminal, was not found in name map.) (Residue 177: ASP, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: GLY, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: GLN, Nonterminal, was not found in name map.) (Residue 183: ASP, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) (Residue 185: LEU, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: VAL, Nonterminal, was not found in name map.) (Residue 188: VAL, Nonterminal, was not found in name map.) (Residue 189: GLU, Nonterminal, was not found in name map.) (Residue 190: GLY, Nonterminal, was not found in name map.) (Residue 191: MET, Nonterminal, was not found in name map.) (Residue 192: GLN, Nonterminal, was not found in name map.) (Residue 193: PHE, Nonterminal, was not found in name map.) (Residue 194: ASP, Nonterminal, was not found in name map.) (Residue 195: ARG, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: TYR, Nonterminal, was not found in name map.) (Residue 198: LEU, Nonterminal, was not found in name map.) (Residue 199: SER, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: TYR, Nonterminal, was not found in name map.) (Residue 202: PHE, Nonterminal, was not found in name map.) (Residue 203: ILE, Nonterminal, was not found in name map.) (Residue 204: ASN, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: PRO, Nonterminal, was not found in name map.) (Residue 207: GLU, Nonterminal, was not found in name map.) (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: GLY, Nonterminal, was not found in name map.) (Residue 210: ALA, Nonterminal, was not found in name map.) (Residue 211: VAL, Nonterminal, was not found in name map.) (Residue 212: GLU, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: GLU, Nonterminal, was not found in name map.) (Residue 215: SER, Nonterminal, was not found in name map.) (Residue 216: PRO, Nonterminal, was not found in name map.) (Residue 217: PHE, Nonterminal, was not found in name map.) (Residue 218: ILE, Nonterminal, was not found in name map.) (Residue 219: LEU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: ASP, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: SER, Nonterminal, was not found in name map.) (Residue 227: ASN, Nonterminal, was not found in name map.) (Residue 228: ILE, Nonterminal, was not found in name map.) (Residue 229: ARG, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: MET, Nonterminal, was not found in name map.) (Residue 232: LEU, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: LEU, Nonterminal, was not found in name map.) (Residue 236: GLU, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: VAL, Nonterminal, was not found in name map.) (Residue 239: ALA, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: GLY, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: PRO, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: ILE, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ALA, Nonterminal, was not found in name map.) (Residue 250: GLU, Nonterminal, was not found in name map.) (Residue 251: ASP, Nonterminal, was not found in name map.) (Residue 252: VAL, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: GLY, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: ALA, Nonterminal, was not found in name map.) (Residue 257: LEU, Nonterminal, was not found in name map.) (Residue 258: ALA, Nonterminal, was not found in name map.) (Residue 259: THR, Nonterminal, was not found in name map.) (Residue 260: LEU, Nonterminal, was not found in name map.) (Residue 261: VAL, Nonterminal, was not found in name map.) (Residue 262: VAL, Nonterminal, was not found in name map.) (Residue 263: ASN, Nonterminal, was not found in name map.) (Residue 264: THR, Nonterminal, was not found in name map.) (Residue 265: MET, Nonterminal, was not found in name map.) (Residue 266: ARG, Nonterminal, was not found in name map.) (Residue 267: GLY, Nonterminal, was not found in name map.) (Residue 268: ILE, Nonterminal, was not found in name map.) (Residue 269: VAL, Nonterminal, was not found in name map.) (Residue 270: LYS, Nonterminal, was not found in name map.) (Residue 271: VAL, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: ALA, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: LYS, Nonterminal, was not found in name map.) (Residue 276: ALA, Nonterminal, was not found in name map.) (Residue 277: PRO, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: PHE, Nonterminal, was not found in name map.) (Residue 280: GLY, Nonterminal, was not found in name map.) (Residue 281: ASP, Nonterminal, was not found in name map.) (Residue 282: ARG, Nonterminal, was not found in name map.) (Residue 283: ARG, Nonterminal, was not found in name map.) (Residue 284: LYS, Nonterminal, was not found in name map.) (Residue 285: ALA, Nonterminal, was not found in name map.) (Residue 286: MET, Nonterminal, was not found in name map.) (Residue 287: LEU, Nonterminal, was not found in name map.) (Residue 288: GLN, Nonterminal, was not found in name map.) (Residue 289: ASP, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: ALA, Nonterminal, was not found in name map.) (Residue 292: THR, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: THR, Nonterminal, was not found in name map.) (Residue 295: GLY, Nonterminal, was not found in name map.) (Residue 296: GLY, Nonterminal, was not found in name map.) (Residue 297: THR, Nonterminal, was not found in name map.) (Residue 298: VAL, Nonterminal, was not found in name map.) (Residue 299: ILE, Nonterminal, was not found in name map.) (Residue 300: SER, Nonterminal, was not found in name map.) (Residue 301: GLU, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: ILE, Nonterminal, was not found in name map.) (Residue 304: GLY, Nonterminal, was not found in name map.) (Residue 305: MET, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: LEU, Nonterminal, was not found in name map.) (Residue 308: GLU, Nonterminal, was not found in name map.) (Residue 309: LYS, Nonterminal, was not found in name map.) (Residue 310: ALA, Nonterminal, was not found in name map.) (Residue 311: THR, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: ASP, Nonterminal, was not found in name map.) (Residue 315: LEU, Nonterminal, was not found in name map.) (Residue 316: GLY, Nonterminal, was not found in name map.) (Residue 317: GLN, Nonterminal, was not found in name map.) (Residue 318: ALA, Nonterminal, was not found in name map.) (Residue 319: LYS, Nonterminal, was not found in name map.) (Residue 320: ARG, Nonterminal, was not found in name map.) (Residue 321: VAL, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: ILE, Nonterminal, was not found in name map.) (Residue 324: ASN, Nonterminal, was not found in name map.) (Residue 325: LYS, Nonterminal, was not found in name map.) (Residue 326: ASP, Nonterminal, was not found in name map.) (Residue 327: THR, Nonterminal, was not found in name map.) (Residue 328: THR, Nonterminal, was not found in name map.) (Residue 329: THR, Nonterminal, was not found in name map.) (Residue 330: ILE, Nonterminal, was not found in name map.) (Residue 331: ILE, Nonterminal, was not found in name map.) (Residue 332: ASP, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: VAL, Nonterminal, was not found in name map.) (Residue 335: GLY, Nonterminal, was not found in name map.) (Residue 336: GLU, Nonterminal, was not found in name map.) (Residue 337: GLU, Nonterminal, was not found in name map.) (Residue 338: ALA, Nonterminal, was not found in name map.) (Residue 339: ALA, Nonterminal, was not found in name map.) (Residue 340: ILE, Nonterminal, was not found in name map.) (Residue 341: GLN, Nonterminal, was not found in name map.) (Residue 342: GLY, Nonterminal, was not found in name map.) (Residue 343: ARG, Nonterminal, was not found in name map.) (Residue 344: VAL, Nonterminal, was not found in name map.) (Residue 345: ALA, Nonterminal, was not found in name map.) (Residue 346: GLN, Nonterminal, was not found in name map.) (Residue 347: ILE, Nonterminal, was not found in name map.) (Residue 348: ARG, Nonterminal, was not found in name map.) (Residue 349: GLN, Nonterminal, was not found in name map.) (Residue 350: GLN, Nonterminal, was not found in name map.) (Residue 351: ILE, Nonterminal, was not found in name map.) (Residue 352: GLU, Nonterminal, was not found in name map.) (Residue 353: GLU, Nonterminal, was not found in name map.) (Residue 354: ALA, Nonterminal, was not found in name map.) (Residue 355: THR, Nonterminal, was not found in name map.) (Residue 356: SER, Nonterminal, was not found in name map.) (Residue 357: ASP, Nonterminal, was not found in name map.) (Residue 358: TYR, Nonterminal, was not found in name map.) (Residue 359: ASP, Nonterminal, was not found in name map.) (Residue 360: ARG, Nonterminal, was not found in name map.) (Residue 361: GLU, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: LEU, Nonterminal, was not found in name map.) (Residue 364: GLN, Nonterminal, was not found in name map.) (Residue 365: GLU, Nonterminal, was not found in name map.) (Residue 366: ARG, Nonterminal, was not found in name map.) (Residue 367: VAL, Nonterminal, was not found in name map.) (Residue 368: ALA, Nonterminal, was not found in name map.) (Residue 369: LYS, Nonterminal, was not found in name map.) (Residue 370: LEU, Nonterminal, was not found in name map.) (Residue 371: ALA, Nonterminal, was not found in name map.) (Residue 372: GLY, Nonterminal, was not found in name map.) (Residue 373: GLY, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: ALA, Nonterminal, was not found in name map.) (Residue 376: VAL, Nonterminal, was not found in name map.) (Residue 377: ILE, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: VAL, Nonterminal, was not found in name map.) (Residue 380: GLY, Nonterminal, was not found in name map.) (Residue 381: ALA, Nonterminal, was not found in name map.) (Residue 382: ALA, Nonterminal, was not found in name map.) (Residue 383: THR, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: VAL, Nonterminal, was not found in name map.) (Residue 386: GLU, Nonterminal, was not found in name map.) (Residue 387: MET, Nonterminal, was not found in name map.) (Residue 388: LYS, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: LYS, Nonterminal, was not found in name map.) (Residue 391: LYS, Nonterminal, was not found in name map.) (Residue 392: ALA, Nonterminal, was not found in name map.) (Residue 393: ARG, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: GLU, Nonterminal, was not found in name map.) (Residue 396: ASP, Nonterminal, was not found in name map.) (Residue 397: ALA, Nonterminal, was not found in name map.) (Residue 398: LEU, Nonterminal, was not found in name map.) (Residue 399: HID, Nonterminal, was not found in name map.) (Residue 400: ALA, Nonterminal, was not found in name map.) (Residue 401: THR, Nonterminal, was not found in name map.) (Residue 402: ARG, Nonterminal, was not found in name map.) (Residue 403: ALA, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: VAL, Nonterminal, was not found in name map.) (Residue 406: GLU, Nonterminal, was not found in name map.) (Residue 407: GLU, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: VAL, Nonterminal, was not found in name map.) (Residue 410: VAL, Nonterminal, was not found in name map.) (Residue 411: ALA, Nonterminal, was not found in name map.) (Residue 412: GLY, Nonterminal, was not found in name map.) (Residue 413: GLY, Nonterminal, was not found in name map.) (Residue 414: GLY, Nonterminal, was not found in name map.) (Residue 415: VAL, Nonterminal, was not found in name map.) (Residue 416: ALA, Nonterminal, was not found in name map.) (Residue 417: LEU, Nonterminal, was not found in name map.) (Residue 418: ILE, Nonterminal, was not found in name map.) (Residue 419: ARG, Nonterminal, was not found in name map.) (Residue 420: VAL, Nonterminal, was not found in name map.) (Residue 421: ALA, Nonterminal, was not found in name map.) (Residue 422: SER, Nonterminal, was not found in name map.) (Residue 423: LYS, Nonterminal, was not found in name map.) (Residue 424: LEU, Nonterminal, was not found in name map.) (Residue 425: ALA, Nonterminal, was not found in name map.) (Residue 426: ASP, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: ARG, Nonterminal, was not found in name map.) (Residue 429: GLY, Nonterminal, was not found in name map.) (Residue 430: GLN, Nonterminal, was not found in name map.) (Residue 431: ASN, Nonterminal, was not found in name map.) (Residue 432: GLU, Nonterminal, was not found in name map.) (Residue 433: ASP, Nonterminal, was not found in name map.) (Residue 434: GLN, Nonterminal, was not found in name map.) (Residue 435: ASN, Nonterminal, was not found in name map.) (Residue 436: VAL, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: ILE, Nonterminal, was not found in name map.) (Residue 439: LYS, Nonterminal, was not found in name map.) (Residue 440: VAL, Nonterminal, was not found in name map.) (Residue 441: ALA, Nonterminal, was not found in name map.) (Residue 442: LEU, Nonterminal, was not found in name map.) (Residue 443: ARG, Nonterminal, was not found in name map.) (Residue 444: ALA, Nonterminal, was not found in name map.) (Residue 445: MET, Nonterminal, was not found in name map.) (Residue 446: GLU, Nonterminal, was not found in name map.) (Residue 447: ALA, Nonterminal, was not found in name map.) (Residue 448: PRO, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: ARG, Nonterminal, was not found in name map.) (Residue 451: GLN, Nonterminal, was not found in name map.) (Residue 452: ILE, Nonterminal, was not found in name map.) (Residue 453: VAL, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: ASN, Nonterminal, was not found in name map.) (Residue 456: CYS, Nonterminal, was not found in name map.) (Residue 457: GLY, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: GLU, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: SER, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: VAL, Nonterminal, was not found in name map.) (Residue 464: ALA, Nonterminal, was not found in name map.) (Residue 465: ASN, Nonterminal, was not found in name map.) (Residue 466: THR, Nonterminal, was not found in name map.) (Residue 467: VAL, Nonterminal, was not found in name map.) (Residue 468: LYS, Nonterminal, was not found in name map.) (Residue 469: GLY, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) (Residue 471: ASP, Nonterminal, was not found in name map.) (Residue 472: GLY, Nonterminal, was not found in name map.) (Residue 473: ASN, Nonterminal, was not found in name map.) (Residue 474: TYR, Nonterminal, was not found in name map.) (Residue 475: GLY, Nonterminal, was not found in name map.) (Residue 476: TYR, Nonterminal, was not found in name map.) (Residue 477: ASN, Nonterminal, was not found in name map.) (Residue 478: ALA, Nonterminal, was not found in name map.) (Residue 479: ALA, Nonterminal, was not found in name map.) (Residue 480: THR, Nonterminal, was not found in name map.) (Residue 481: GLU, Nonterminal, was not found in name map.) (Residue 482: GLU, Nonterminal, was not found in name map.) (Residue 483: TYR, Nonterminal, was not found in name map.) (Residue 484: GLY, Nonterminal, was not found in name map.) (Residue 485: ASN, Nonterminal, was not found in name map.) (Residue 486: MET, Nonterminal, was not found in name map.) (Residue 487: ILE, Nonterminal, was not found in name map.) (Residue 488: ASP, Nonterminal, was not found in name map.) (Residue 489: MET, Nonterminal, was not found in name map.) (Residue 490: GLY, Nonterminal, was not found in name map.) (Residue 491: ILE, Nonterminal, was not found in name map.) (Residue 492: LEU, Nonterminal, was not found in name map.) (Residue 493: ASP, Nonterminal, was not found in name map.) (Residue 494: PRO, Nonterminal, was not found in name map.) (Residue 495: THR, Nonterminal, was not found in name map.) (Residue 496: LYS, Nonterminal, was not found in name map.) (Residue 497: VAL, Nonterminal, was not found in name map.) (Residue 498: THR, Nonterminal, was not found in name map.) (Residue 499: ARG, Nonterminal, was not found in name map.) (Residue 500: SER, Nonterminal, was not found in name map.) (Residue 501: ALA, Nonterminal, was not found in name map.) (Residue 502: LEU, Nonterminal, was not found in name map.) (Residue 503: GLN, Nonterminal, was not found in name map.) (Residue 504: TYR, Nonterminal, was not found in name map.) (Residue 505: ALA, Nonterminal, was not found in name map.) (Residue 506: ALA, Nonterminal, was not found in name map.) (Residue 507: SER, Nonterminal, was not found in name map.) (Residue 508: VAL, Nonterminal, was not found in name map.) (Residue 509: ALA, Nonterminal, was not found in name map.) (Residue 510: GLY, Nonterminal, was not found in name map.) (Residue 511: LEU, Nonterminal, was not found in name map.) (Residue 512: MET, Nonterminal, was not found in name map.) (Residue 513: ILE, Nonterminal, was not found in name map.) (Residue 514: THR, Nonterminal, was not found in name map.) (Residue 515: THR, Nonterminal, was not found in name map.) (Residue 516: GLU, Nonterminal, was not found in name map.) (Residue 517: CYS, Nonterminal, was not found in name map.) (Residue 518: MET, Nonterminal, was not found in name map.) (Residue 519: VAL, Nonterminal, was not found in name map.) (Residue 520: THR, Nonterminal, was not found in name map.) (Residue 521: ASP, Nonterminal, was not found in name map.) (Residue 522: LEU, Nonterminal, was not found in name map.) Mapped residue PRO, term: Terminal/last, seq. number: 523 to: CPRO. Joining NALA - ALA Joining ALA - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - GLY Joining GLY - VAL Joining VAL - LYS Joining LYS - MET Joining MET - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - THR Joining THR - LEU Joining LEU - GLY Joining GLY - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - PRO Joining PRO - THR Joining THR - ILE Joining ILE - THR Joining THR - LYS Joining LYS - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - SER Joining SER - VAL Joining VAL - ALA Joining ALA - ARG Joining ARG - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LYS Joining LYS - PHE Joining PHE - GLU Joining GLU - ASN Joining ASN - MET Joining MET - GLY Joining GLY - ALA Joining ALA - GLN Joining GLN - MET Joining MET - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - THR Joining THR - THR Joining THR - THR Joining THR - ALA Joining ALA - THR Joining THR - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - ALA Joining ALA - ILE Joining ILE - ILE Joining ILE - THR Joining THR - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - MET Joining MET - ASN Joining ASN - PRO Joining PRO - MET Joining MET - ASP Joining ASP - LEU Joining LEU - LYS Joining LYS - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - THR Joining THR - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - VAL Joining VAL - PRO Joining PRO - CYS Joining CYS - SER Joining SER - ASP Joining ASP - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - GLY Joining GLY - THR Joining THR - ILE Joining ILE - SER Joining SER - ALA Joining ALA - ASN Joining ASN - SER Joining SER - ASP Joining ASP - GLU Joining GLU - THR Joining THR - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - MET Joining MET - ASP Joining ASP - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - THR Joining THR - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - GLY Joining GLY - THR Joining THR - GLY Joining GLY - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - MET Joining MET - GLN Joining GLN - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - PRO Joining PRO - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - THR Joining THR - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - SER Joining SER - PRO Joining PRO - PHE Joining PHE - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LYS Joining LYS - LYS Joining LYS - ILE Joining ILE - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ARG Joining ARG - GLU Joining GLU - MET Joining MET - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - THR Joining THR - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - THR Joining THR - MET Joining MET - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ARG Joining ARG - ARG Joining ARG - LYS Joining LYS - ALA Joining ALA - MET Joining MET - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - ALA Joining ALA - THR Joining THR - LEU Joining LEU - THR Joining THR - GLY Joining GLY - GLY Joining GLY - THR Joining THR - VAL Joining VAL - ILE Joining ILE - SER Joining SER - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - GLY Joining GLY - MET Joining MET - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLY Joining GLY - GLN Joining GLN - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - THR Joining THR - THR Joining THR - THR Joining THR - ILE Joining ILE - ILE Joining ILE - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - ILE Joining ILE - GLN Joining GLN - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - ILE Joining ILE - ARG Joining ARG - GLN Joining GLN - GLN Joining GLN - ILE Joining ILE - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - THR Joining THR - SER Joining SER - ASP Joining ASP - TYR Joining TYR - ASP Joining ASP - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - VAL Joining VAL - GLU Joining GLU - MET Joining MET - LYS Joining LYS - GLU Joining GLU - LYS Joining LYS - LYS Joining LYS - ALA Joining ALA - ARG Joining ARG - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ALA Joining ALA - THR Joining THR - ARG Joining ARG - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - GLN Joining GLN - ASN Joining ASN - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Joining ASP - GLN Joining GLN - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - ALA Joining ALA - MET Joining MET - GLU Joining GLU - ALA Joining ALA - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - GLN Joining GLN - ILE Joining ILE - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - TYR Joining TYR - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - GLU Joining GLU - TYR Joining TYR - GLY Joining GLY - ASN Joining ASN - MET Joining MET - ILE Joining ILE - ASP Joining ASP - MET Joining MET - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - THR Joining THR - LYS Joining LYS - VAL Joining VAL - THR Joining THR - ARG Joining ARG - SER Joining SER - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - TYR Joining TYR - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - LEU Joining LEU - MET Joining MET - ILE Joining ILE - THR Joining THR - THR Joining THR - GLU Joining GLU - CYS Joining CYS - MET Joining MET - VAL Joining VAL - THR Joining THR - ASP Joining ASP - LEU Joining LEU - CPRO Added missing heavy atom: .R.A total atoms in file: 3846 Leap added 3978 missing atoms according to residue templates: 5 Heavy 3973 H / lone pairs > > #w = loadpdb waters_with_hbond_after_min_sol.pdb > #mol = combine {mol w} > > saveamberparm mol 2C7E_chainA_noWAT.prmtop 2C7E_chainA_noWAT.inpcrd Checking Unit. WARNING: There is a bond of 4.940917 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 8.152534 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -19.000003 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. total 1366 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 CPRO 1 NALA 1 ) (no restraints) log started: Wed Jun 23 15:23:16 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) 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" } >> { "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" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /net/bccs/cbu/linux64/amber11/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: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /net/bccs/cbu/linux64/amber11/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /net/bccs/cbu/linux64/amber11/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: /net/bccs/cbu/linux64/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /net/bccs/cbu/linux64/amber11/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. >> # >> loadOff all_aminoct03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminoct03.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS 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 >> loadOff all_aminont03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_aminont03.lib Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS 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 >> loadOff all_amino03.lib Loading library: /net/bccs/cbu/linux64/amber11/dat/leap/lib/all_amino03.lib Loading: ACE 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> >> # >> # 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" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > mol = loadpdb 2C7E_A.pdb_flsq.pdb Loading PDB file: ./2C7E_A.pdb_flsq.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: LYS, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: GLY, Nonterminal, was not found in name map.) (Residue 8: ASN, Nonterminal, was not found in name map.) (Residue 9: ASP, Nonterminal, was not found in name map.) (Residue 10: ALA, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: LYS, Nonterminal, was not found in name map.) (Residue 14: MET, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: ARG, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: VAL, Nonterminal, was not found in name map.) (Residue 19: ASN, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ALA, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ALA, Nonterminal, was not found in name map.) (Residue 25: VAL, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: VAL, Nonterminal, was not found in name map.) (Residue 28: THR, Nonterminal, was not found in name map.) (Residue 29: LEU, Nonterminal, was not found in name map.) (Residue 30: GLY, Nonterminal, was not found in name map.) (Residue 31: PRO, Nonterminal, was not found in name map.) (Residue 32: LYS, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ARG, Nonterminal, was not found in name map.) (Residue 35: ASN, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: VAL, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: ASP, Nonterminal, was not found in name map.) (Residue 40: LYS, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: PHE, Nonterminal, was not found in name map.) (Residue 43: GLY, Nonterminal, was not found in name map.) (Residue 44: ALA, Nonterminal, was not found in name map.) (Residue 45: PRO, Nonterminal, was not found in name map.) (Residue 46: THR, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: LYS, Nonterminal, was not found in name map.) (Residue 50: ASP, Nonterminal, was not found in name map.) (Residue 51: GLY, Nonterminal, was not found in name map.) (Residue 52: VAL, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: VAL, Nonterminal, was not found in name map.) (Residue 55: ALA, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: GLU, Nonterminal, was not found in name map.) (Residue 58: ILE, Nonterminal, was not found in name map.) (Residue 59: GLU, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: GLU, Nonterminal, was not found in name map.) (Residue 62: ASP, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: GLU, Nonterminal, was not found in name map.) (Residue 66: ASN, Nonterminal, was not found in name map.) (Residue 67: MET, Nonterminal, was not found in name map.) (Residue 68: GLY, Nonterminal, was not found in name map.) (Residue 69: ALA, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: MET, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: LYS, Nonterminal, was not found in name map.) (Residue 74: GLU, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: ALA, Nonterminal, was not found in name map.) (Residue 77: SER, Nonterminal, was not found in name map.) (Residue 78: LYS, Nonterminal, was not found in name map.) (Residue 79: ALA, Nonterminal, was not found in name map.) (Residue 80: ASN, Nonterminal, was not found in name map.) (Residue 81: ASP, Nonterminal, was not found in name map.) (Residue 82: ALA, Nonterminal, was not found in name map.) (Residue 83: ALA, Nonterminal, was not found in name map.) (Residue 84: GLY, Nonterminal, was not found in name map.) (Residue 85: ASP, Nonterminal, was not found in name map.) (Residue 86: GLY, Nonterminal, was not found in name map.) (Residue 87: THR, Nonterminal, was not found in name map.) (Residue 88: THR, Nonterminal, was not found in name map.) (Residue 89: THR, Nonterminal, was not found in name map.) (Residue 90: ALA, Nonterminal, was not found in name map.) (Residue 91: THR, Nonterminal, was not found in name map.) (Residue 92: VAL, Nonterminal, was not found in name map.) (Residue 93: LEU, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLN, Nonterminal, was not found in name map.) (Residue 96: ALA, Nonterminal, was not found in name map.) (Residue 97: ILE, Nonterminal, was not found in name map.) (Residue 98: ILE, Nonterminal, was not found in name map.) (Residue 99: THR, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: GLY, Nonterminal, was not found in name map.) (Residue 102: LEU, Nonterminal, was not found in name map.) (Residue 103: LYS, Nonterminal, was not found in name map.) (Residue 104: ALA, Nonterminal, was not found in name map.) (Residue 105: VAL, Nonterminal, was not found in name map.) (Residue 106: ALA, Nonterminal, was not found in name map.) (Residue 107: ALA, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: MET, Nonterminal, was not found in name map.) (Residue 110: ASN, Nonterminal, was not found in name map.) (Residue 111: PRO, Nonterminal, was not found in name map.) (Residue 112: MET, Nonterminal, was not found in name map.) (Residue 113: ASP, 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: ARG, Nonterminal, was not found in name map.) (Residue 117: GLY, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: ASP, Nonterminal, was not found in name map.) (Residue 120: LYS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: VAL, Nonterminal, was not found in name map.) (Residue 123: THR, Nonterminal, was not found in name map.) (Residue 124: VAL, Nonterminal, was not found in name map.) (Residue 125: ALA, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: GLU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: LYS, Nonterminal, was not found in name map.) (Residue 131: ALA, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: SER, Nonterminal, was not found in name map.) (Residue 134: VAL, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: CYS, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: ASP, Nonterminal, was not found in name map.) (Residue 139: SER, Nonterminal, was not found in name map.) (Residue 140: LYS, Nonterminal, was not found in name map.) (Residue 141: ALA, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: GLN, Nonterminal, was not found in name map.) (Residue 145: VAL, Nonterminal, was not found in name map.) (Residue 146: GLY, Nonterminal, was not found in name map.) (Residue 147: THR, Nonterminal, was not found in name map.) (Residue 148: ILE, Nonterminal, was not found in name map.) (Residue 149: SER, Nonterminal, was not found in name map.) (Residue 150: ALA, Nonterminal, was not found in name map.) (Residue 151: ASN, Nonterminal, was not found in name map.) (Residue 152: SER, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: GLU, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: VAL, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: LEU, Nonterminal, was not found in name map.) (Residue 160: ILE, Nonterminal, was not found in name map.) (Residue 161: ALA, Nonterminal, was not found in name map.) (Residue 162: GLU, Nonterminal, was not found in name map.) (Residue 163: ALA, Nonterminal, was not found in name map.) (Residue 164: MET, Nonterminal, was not found in name map.) (Residue 165: ASP, Nonterminal, was not found in name map.) (Residue 166: LYS, Nonterminal, was not found in name map.) (Residue 167: VAL, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: LYS, Nonterminal, was not found in name map.) (Residue 170: GLU, Nonterminal, was not found in name map.) (Residue 171: GLY, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: ILE, Nonterminal, was not found in name map.) (Residue 174: THR, Nonterminal, was not found in name map.) (Residue 175: VAL, Nonterminal, was not found in name map.) (Residue 176: GLU, Nonterminal, was not found in name map.) (Residue 177: ASP, Nonterminal, was not found in name map.) (Residue 178: GLY, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: GLY, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: GLN, Nonterminal, was not found in name map.) (Residue 183: ASP, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) (Residue 185: LEU, Nonterminal, was not found in name map.) (Residue 186: ASP, Nonterminal, was not found in name map.) (Residue 187: VAL, Nonterminal, was not found in name map.) (Residue 188: VAL, Nonterminal, was not found in name map.) (Residue 189: GLU, Nonterminal, was not found in name map.) (Residue 190: GLY, Nonterminal, was not found in name map.) (Residue 191: MET, Nonterminal, was not found in name map.) (Residue 192: GLN, Nonterminal, was not found in name map.) (Residue 193: PHE, Nonterminal, was not found in name map.) (Residue 194: ASP, Nonterminal, was not found in name map.) (Residue 195: ARG, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: TYR, Nonterminal, was not found in name map.) (Residue 198: LEU, Nonterminal, was not found in name map.) (Residue 199: SER, Nonterminal, was not found in name map.) (Residue 200: PRO, Nonterminal, was not found in name map.) (Residue 201: TYR, Nonterminal, was not found in name map.) (Residue 202: PHE, Nonterminal, was not found in name map.) (Residue 203: ILE, Nonterminal, was not found in name map.) (Residue 204: ASN, Nonterminal, was not found in name map.) (Residue 205: LYS, Nonterminal, was not found in name map.) (Residue 206: PRO, Nonterminal, was not found in name map.) (Residue 207: GLU, Nonterminal, was not found in name map.) (Residue 208: THR, Nonterminal, was not found in name map.) (Residue 209: GLY, Nonterminal, was not found in name map.) (Residue 210: ALA, Nonterminal, was not found in name map.) (Residue 211: VAL, Nonterminal, was not found in name map.) (Residue 212: GLU, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: GLU, Nonterminal, was not found in name map.) (Residue 215: SER, Nonterminal, was not found in name map.) (Residue 216: PRO, Nonterminal, was not found in name map.) (Residue 217: PHE, Nonterminal, was not found in name map.) (Residue 218: ILE, Nonterminal, was not found in name map.) (Residue 219: LEU, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: ASP, Nonterminal, was not found in name map.) (Residue 223: LYS, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: SER, Nonterminal, was not found in name map.) (Residue 227: ASN, Nonterminal, was not found in name map.) (Residue 228: ILE, Nonterminal, was not found in name map.) (Residue 229: ARG, Nonterminal, was not found in name map.) (Residue 230: GLU, Nonterminal, was not found in name map.) (Residue 231: MET, Nonterminal, was not found in name map.) (Residue 232: LEU, Nonterminal, was not found in name map.) (Residue 233: PRO, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: LEU, Nonterminal, was not found in name map.) (Residue 236: GLU, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: VAL, Nonterminal, was not found in name map.) (Residue 239: ALA, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: GLY, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: PRO, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: LEU, Nonterminal, was not found in name map.) (Residue 247: ILE, Nonterminal, was not found in name map.) (Residue 248: ILE, Nonterminal, was not found in name map.) (Residue 249: ALA, Nonterminal, was not found in name map.) (Residue 250: GLU, Nonterminal, was not found in name map.) (Residue 251: ASP, Nonterminal, was not found in name map.) (Residue 252: VAL, Nonterminal, was not found in name map.) (Residue 253: GLU, Nonterminal, was not found in name map.) (Residue 254: GLY, Nonterminal, was not found in name map.) (Residue 255: GLU, Nonterminal, was not found in name map.) (Residue 256: ALA, Nonterminal, was not found in name map.) (Residue 257: LEU, Nonterminal, was not found in name map.) (Residue 258: ALA, Nonterminal, was not found in name map.) (Residue 259: THR, Nonterminal, was not found in name map.) (Residue 260: LEU, Nonterminal, was not found in name map.) (Residue 261: VAL, Nonterminal, was not found in name map.) (Residue 262: VAL, Nonterminal, was not found in name map.) (Residue 263: ASN, Nonterminal, was not found in name map.) (Residue 264: THR, Nonterminal, was not found in name map.) (Residue 265: MET, Nonterminal, was not found in name map.) (Residue 266: ARG, Nonterminal, was not found in name map.) (Residue 267: GLY, Nonterminal, was not found in name map.) (Residue 268: ILE, Nonterminal, was not found in name map.) (Residue 269: VAL, Nonterminal, was not found in name map.) (Residue 270: LYS, Nonterminal, was not found in name map.) (Residue 271: VAL, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: ALA, Nonterminal, was not found in name map.) (Residue 274: VAL, Nonterminal, was not found in name map.) (Residue 275: LYS, Nonterminal, was not found in name map.) (Residue 276: ALA, Nonterminal, was not found in name map.) (Residue 277: PRO, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: PHE, Nonterminal, was not found in name map.) (Residue 280: GLY, Nonterminal, was not found in name map.) (Residue 281: ASP, Nonterminal, was not found in name map.) (Residue 282: ARG, Nonterminal, was not found in name map.) (Residue 283: ARG, Nonterminal, was not found in name map.) (Residue 284: LYS, Nonterminal, was not found in name map.) (Residue 285: ALA, Nonterminal, was not found in name map.) (Residue 286: MET, Nonterminal, was not found in name map.) (Residue 287: LEU, Nonterminal, was not found in name map.) (Residue 288: GLN, Nonterminal, was not found in name map.) (Residue 289: ASP, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: ALA, Nonterminal, was not found in name map.) (Residue 292: THR, Nonterminal, was not found in name map.) (Residue 293: LEU, Nonterminal, was not found in name map.) (Residue 294: THR, Nonterminal, was not found in name map.) (Residue 295: GLY, Nonterminal, was not found in name map.) (Residue 296: GLY, Nonterminal, was not found in name map.) (Residue 297: THR, Nonterminal, was not found in name map.) (Residue 298: VAL, Nonterminal, was not found in name map.) (Residue 299: ILE, Nonterminal, was not found in name map.) (Residue 300: SER, Nonterminal, was not found in name map.) (Residue 301: GLU, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: ILE, Nonterminal, was not found in name map.) (Residue 304: GLY, Nonterminal, was not found in name map.) (Residue 305: MET, Nonterminal, was not found in name map.) (Residue 306: GLU, Nonterminal, was not found in name map.) (Residue 307: LEU, Nonterminal, was not found in name map.) (Residue 308: GLU, Nonterminal, was not found in name map.) (Residue 309: LYS, Nonterminal, was not found in name map.) (Residue 310: ALA, Nonterminal, was not found in name map.) (Residue 311: THR, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: ASP, Nonterminal, was not found in name map.) (Residue 315: LEU, Nonterminal, was not found in name map.) (Residue 316: GLY, Nonterminal, was not found in name map.) (Residue 317: GLN, Nonterminal, was not found in name map.) (Residue 318: ALA, Nonterminal, was not found in name map.) (Residue 319: LYS, Nonterminal, was not found in name map.) (Residue 320: ARG, Nonterminal, was not found in name map.) (Residue 321: VAL, Nonterminal, was not found in name map.) (Residue 322: VAL, Nonterminal, was not found in name map.) (Residue 323: ILE, Nonterminal, was not found in name map.) (Residue 324: ASN, Nonterminal, was not found in name map.) (Residue 325: LYS, Nonterminal, was not found in name map.) (Residue 326: ASP, Nonterminal, was not found in name map.) (Residue 327: THR, Nonterminal, was not found in name map.) (Residue 328: THR, Nonterminal, was not found in name map.) (Residue 329: THR, Nonterminal, was not found in name map.) (Residue 330: ILE, Nonterminal, was not found in name map.) (Residue 331: ILE, Nonterminal, was not found in name map.) (Residue 332: ASP, Nonterminal, was not found in name map.) (Residue 333: GLY, Nonterminal, was not found in name map.) (Residue 334: VAL, Nonterminal, was not found in name map.) (Residue 335: GLY, Nonterminal, was not found in name map.) (Residue 336: GLU, Nonterminal, was not found in name map.) (Residue 337: GLU, Nonterminal, was not found in name map.) (Residue 338: ALA, Nonterminal, was not found in name map.) (Residue 339: ALA, Nonterminal, was not found in name map.) (Residue 340: ILE, Nonterminal, was not found in name map.) (Residue 341: GLN, Nonterminal, was not found in name map.) (Residue 342: GLY, Nonterminal, was not found in name map.) (Residue 343: ARG, Nonterminal, was not found in name map.) (Residue 344: VAL, Nonterminal, was not found in name map.) (Residue 345: ALA, Nonterminal, was not found in name map.) (Residue 346: GLN, Nonterminal, was not found in name map.) (Residue 347: ILE, Nonterminal, was not found in name map.) (Residue 348: ARG, Nonterminal, was not found in name map.) (Residue 349: GLN, Nonterminal, was not found in name map.) (Residue 350: GLN, Nonterminal, was not found in name map.) (Residue 351: ILE, Nonterminal, was not found in name map.) (Residue 352: GLU, Nonterminal, was not found in name map.) (Residue 353: GLU, Nonterminal, was not found in name map.) (Residue 354: ALA, Nonterminal, was not found in name map.) (Residue 355: THR, Nonterminal, was not found in name map.) (Residue 356: SER, Nonterminal, was not found in name map.) (Residue 357: ASP, Nonterminal, was not found in name map.) (Residue 358: TYR, Nonterminal, was not found in name map.) (Residue 359: ASP, Nonterminal, was not found in name map.) (Residue 360: ARG, Nonterminal, was not found in name map.) (Residue 361: GLU, Nonterminal, was not found in name map.) (Residue 362: LYS, Nonterminal, was not found in name map.) (Residue 363: LEU, Nonterminal, was not found in name map.) (Residue 364: GLN, Nonterminal, was not found in name map.) (Residue 365: GLU, Nonterminal, was not found in name map.) (Residue 366: ARG, Nonterminal, was not found in name map.) (Residue 367: VAL, Nonterminal, was not found in name map.) (Residue 368: ALA, Nonterminal, was not found in name map.) (Residue 369: LYS, Nonterminal, was not found in name map.) (Residue 370: LEU, Nonterminal, was not found in name map.) (Residue 371: ALA, Nonterminal, was not found in name map.) (Residue 372: GLY, Nonterminal, was not found in name map.) (Residue 373: GLY, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: ALA, Nonterminal, was not found in name map.) (Residue 376: VAL, Nonterminal, was not found in name map.) (Residue 377: ILE, Nonterminal, was not found in name map.) (Residue 378: LYS, Nonterminal, was not found in name map.) (Residue 379: VAL, Nonterminal, was not found in name map.) (Residue 380: GLY, Nonterminal, was not found in name map.) (Residue 381: ALA, Nonterminal, was not found in name map.) (Residue 382: ALA, Nonterminal, was not found in name map.) (Residue 383: THR, Nonterminal, was not found in name map.) (Residue 384: GLU, Nonterminal, was not found in name map.) (Residue 385: VAL, Nonterminal, was not found in name map.) (Residue 386: GLU, Nonterminal, was not found in name map.) (Residue 387: MET, Nonterminal, was not found in name map.) (Residue 388: LYS, Nonterminal, was not found in name map.) (Residue 389: GLU, Nonterminal, was not found in name map.) (Residue 390: LYS, Nonterminal, was not found in name map.) (Residue 391: LYS, Nonterminal, was not found in name map.) (Residue 392: ALA, Nonterminal, was not found in name map.) (Residue 393: ARG, Nonterminal, was not found in name map.) (Residue 394: VAL, Nonterminal, was not found in name map.) (Residue 395: GLU, Nonterminal, was not found in name map.) (Residue 396: ASP, Nonterminal, was not found in name map.) (Residue 397: ALA, Nonterminal, was not found in name map.) (Residue 398: LEU, Nonterminal, was not found in name map.) (Residue 399: HID, Nonterminal, was not found in name map.) (Residue 400: ALA, Nonterminal, was not found in name map.) (Residue 401: THR, Nonterminal, was not found in name map.) (Residue 402: ARG, Nonterminal, was not found in name map.) (Residue 403: ALA, Nonterminal, was not found in name map.) (Residue 404: ALA, Nonterminal, was not found in name map.) (Residue 405: VAL, Nonterminal, was not found in name map.) (Residue 406: GLU, Nonterminal, was not found in name map.) (Residue 407: GLU, Nonterminal, was not found in name map.) (Residue 408: GLY, Nonterminal, was not found in name map.) (Residue 409: VAL, Nonterminal, was not found in name map.) (Residue 410: VAL, Nonterminal, was not found in name map.) (Residue 411: ALA, Nonterminal, was not found in name map.) (Residue 412: GLY, Nonterminal, was not found in name map.) (Residue 413: GLY, Nonterminal, was not found in name map.) (Residue 414: GLY, Nonterminal, was not found in name map.) (Residue 415: VAL, Nonterminal, was not found in name map.) (Residue 416: ALA, Nonterminal, was not found in name map.) (Residue 417: LEU, Nonterminal, was not found in name map.) (Residue 418: ILE, Nonterminal, was not found in name map.) (Residue 419: ARG, Nonterminal, was not found in name map.) (Residue 420: VAL, Nonterminal, was not found in name map.) (Residue 421: ALA, Nonterminal, was not found in name map.) (Residue 422: SER, Nonterminal, was not found in name map.) (Residue 423: LYS, Nonterminal, was not found in name map.) (Residue 424: LEU, Nonterminal, was not found in name map.) (Residue 425: ALA, Nonterminal, was not found in name map.) (Residue 426: ASP, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: ARG, Nonterminal, was not found in name map.) (Residue 429: GLY, Nonterminal, was not found in name map.) (Residue 430: GLN, Nonterminal, was not found in name map.) (Residue 431: ASN, Nonterminal, was not found in name map.) (Residue 432: GLU, Nonterminal, was not found in name map.) (Residue 433: ASP, Nonterminal, was not found in name map.) (Residue 434: GLN, Nonterminal, was not found in name map.) (Residue 435: ASN, Nonterminal, was not found in name map.) (Residue 436: VAL, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: ILE, Nonterminal, was not found in name map.) (Residue 439: LYS, Nonterminal, was not found in name map.) (Residue 440: VAL, Nonterminal, was not found in name map.) (Residue 441: ALA, Nonterminal, was not found in name map.) (Residue 442: LEU, Nonterminal, was not found in name map.) (Residue 443: ARG, Nonterminal, was not found in name map.) (Residue 444: ALA, Nonterminal, was not found in name map.) (Residue 445: MET, Nonterminal, was not found in name map.) (Residue 446: GLU, Nonterminal, was not found in name map.) (Residue 447: ALA, Nonterminal, was not found in name map.) (Residue 448: PRO, Nonterminal, was not found in name map.) (Residue 449: LEU, Nonterminal, was not found in name map.) (Residue 450: ARG, Nonterminal, was not found in name map.) (Residue 451: GLN, Nonterminal, was not found in name map.) (Residue 452: ILE, Nonterminal, was not found in name map.) (Residue 453: VAL, Nonterminal, was not found in name map.) (Residue 454: LEU, Nonterminal, was not found in name map.) (Residue 455: ASN, Nonterminal, was not found in name map.) (Residue 456: CYS, Nonterminal, was not found in name map.) (Residue 457: GLY, Nonterminal, was not found in name map.) (Residue 458: GLU, Nonterminal, was not found in name map.) (Residue 459: GLU, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: SER, Nonterminal, was not found in name map.) (Residue 462: VAL, Nonterminal, was not found in name map.) (Residue 463: VAL, Nonterminal, was not found in name map.) (Residue 464: ALA, Nonterminal, was not found in name map.) (Residue 465: ASN, Nonterminal, was not found in name map.) (Residue 466: THR, Nonterminal, was not found in name map.) (Residue 467: VAL, Nonterminal, was not found in name map.) (Residue 468: LYS, Nonterminal, was not found in name map.) (Residue 469: GLY, Nonterminal, was not found in name map.) (Residue 470: GLY, Nonterminal, was not found in name map.) (Residue 471: ASP, Nonterminal, was not found in name map.) (Residue 472: GLY, Nonterminal, was not found in name map.) (Residue 473: ASN, Nonterminal, was not found in name map.) (Residue 474: TYR, Nonterminal, was not found in name map.) (Residue 475: GLY, Nonterminal, was not found in name map.) (Residue 476: TYR, Nonterminal, was not found in name map.) (Residue 477: ASN, Nonterminal, was not found in name map.) (Residue 478: ALA, Nonterminal, was not found in name map.) (Residue 479: ALA, Nonterminal, was not found in name map.) (Residue 480: THR, Nonterminal, was not found in name map.) (Residue 481: GLU, Nonterminal, was not found in name map.) (Residue 482: GLU, Nonterminal, was not found in name map.) (Residue 483: TYR, Nonterminal, was not found in name map.) (Residue 484: GLY, Nonterminal, was not found in name map.) (Residue 485: ASN, Nonterminal, was not found in name map.) (Residue 486: MET, Nonterminal, was not found in name map.) (Residue 487: ILE, Nonterminal, was not found in name map.) (Residue 488: ASP, Nonterminal, was not found in name map.) (Residue 489: MET, Nonterminal, was not found in name map.) (Residue 490: GLY, Nonterminal, was not found in name map.) (Residue 491: ILE, Nonterminal, was not found in name map.) (Residue 492: LEU, Nonterminal, was not found in name map.) (Residue 493: ASP, Nonterminal, was not found in name map.) (Residue 494: PRO, Nonterminal, was not found in name map.) (Residue 495: THR, Nonterminal, was not found in name map.) (Residue 496: LYS, Nonterminal, was not found in name map.) (Residue 497: VAL, Nonterminal, was not found in name map.) (Residue 498: THR, Nonterminal, was not found in name map.) (Residue 499: ARG, Nonterminal, was not found in name map.) (Residue 500: SER, Nonterminal, was not found in name map.) (Residue 501: ALA, Nonterminal, was not found in name map.) (Residue 502: LEU, Nonterminal, was not found in name map.) (Residue 503: GLN, Nonterminal, was not found in name map.) (Residue 504: TYR, Nonterminal, was not found in name map.) (Residue 505: ALA, Nonterminal, was not found in name map.) (Residue 506: ALA, Nonterminal, was not found in name map.) (Residue 507: SER, Nonterminal, was not found in name map.) (Residue 508: VAL, Nonterminal, was not found in name map.) (Residue 509: ALA, Nonterminal, was not found in name map.) (Residue 510: GLY, Nonterminal, was not found in name map.) (Residue 511: LEU, Nonterminal, was not found in name map.) (Residue 512: MET, Nonterminal, was not found in name map.) (Residue 513: ILE, Nonterminal, was not found in name map.) (Residue 514: THR, Nonterminal, was not found in name map.) (Residue 515: THR, Nonterminal, was not found in name map.) (Residue 516: GLU, Nonterminal, was not found in name map.) (Residue 517: CYS, Nonterminal, was not found in name map.) (Residue 518: MET, Nonterminal, was not found in name map.) (Residue 519: VAL, Nonterminal, was not found in name map.) (Residue 520: THR, Nonterminal, was not found in name map.) (Residue 521: ASP, Nonterminal, was not found in name map.) (Residue 522: LEU, Nonterminal, was not found in name map.) Mapped residue PRO, term: Terminal/last, seq. number: 523 to: CPRO. Joining NALA - ALA Joining ALA - LYS Joining LYS - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - PHE Joining PHE - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - GLY Joining GLY - VAL Joining VAL - LYS Joining LYS - MET Joining MET - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - THR Joining THR - LEU Joining LEU - GLY Joining GLY - PRO Joining PRO - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - ASP Joining ASP - LYS Joining LYS - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ALA Joining ALA - PRO Joining PRO - THR Joining THR - ILE Joining ILE - THR Joining THR - LYS Joining LYS - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - SER Joining SER - VAL Joining VAL - ALA Joining ALA - ARG Joining ARG - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LYS Joining LYS - PHE Joining PHE - GLU Joining GLU - ASN Joining ASN - MET Joining MET - GLY Joining GLY - ALA Joining ALA - GLN Joining GLN - MET Joining MET - VAL Joining VAL - LYS Joining LYS - GLU Joining GLU - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ASN Joining ASN - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - THR Joining THR - THR Joining THR - THR Joining THR - ALA Joining ALA - THR Joining THR - VAL Joining VAL - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - ALA Joining ALA - ILE Joining ILE - ILE Joining ILE - THR Joining THR - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - MET Joining MET - ASN Joining ASN - PRO Joining PRO - MET Joining MET - ASP Joining ASP - LEU Joining LEU - LYS Joining LYS - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - LYS Joining LYS - ALA Joining ALA - VAL Joining VAL - THR Joining THR - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - SER Joining SER - VAL Joining VAL - PRO Joining PRO - CYS Joining CYS - SER Joining SER - ASP Joining ASP - SER Joining SER - LYS Joining LYS - ALA Joining ALA - ILE Joining ILE - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - GLY Joining GLY - THR Joining THR - ILE Joining ILE - SER Joining SER - ALA Joining ALA - ASN Joining ASN - SER Joining SER - ASP Joining ASP - GLU Joining GLU - THR Joining THR - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - MET Joining MET - ASP Joining ASP - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - LYS Joining LYS - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - ILE Joining ILE - THR Joining THR - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - GLY Joining GLY - THR Joining THR - GLY Joining GLY - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - VAL Joining VAL - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - MET Joining MET - GLN Joining GLN - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - SER Joining SER - PRO Joining PRO - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - PRO Joining PRO - GLU Joining GLU - THR Joining THR - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - SER Joining SER - PRO Joining PRO - PHE Joining PHE - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LYS Joining LYS - LYS Joining LYS - ILE Joining ILE - SER Joining SER - ASN Joining ASN - ILE Joining ILE - ARG Joining ARG - GLU Joining GLU - MET Joining MET - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - ALA Joining ALA - GLY Joining GLY - LYS Joining LYS - PRO Joining PRO - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ASP Joining ASP - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - ALA Joining ALA - THR Joining THR - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - THR Joining THR - MET Joining MET - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - VAL Joining VAL - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - GLY Joining GLY - ASP Joining ASP - ARG Joining ARG - ARG Joining ARG - LYS Joining LYS - ALA Joining ALA - MET Joining MET - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - ALA Joining ALA - THR Joining THR - LEU Joining LEU - THR Joining THR - GLY Joining GLY - GLY Joining GLY - THR Joining THR - VAL Joining VAL - ILE Joining ILE - SER Joining SER - GLU Joining GLU - GLU Joining GLU - ILE Joining ILE - GLY Joining GLY - MET Joining MET - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - LYS Joining LYS - ALA Joining ALA - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLY Joining GLY - GLN Joining GLN - ALA Joining ALA - LYS Joining LYS - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ILE Joining ILE - ASN Joining ASN - LYS Joining LYS - ASP Joining ASP - THR Joining THR - THR Joining THR - THR Joining THR - ILE Joining ILE - ILE Joining ILE - ASP Joining ASP - GLY Joining GLY - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - ILE Joining ILE - GLN Joining GLN - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - ILE Joining ILE - ARG Joining ARG - GLN Joining GLN - GLN Joining GLN - ILE Joining ILE - GLU Joining GLU - GLU Joining GLU - ALA Joining ALA - THR Joining THR - SER Joining SER - ASP Joining ASP - TYR Joining TYR - ASP Joining ASP - ARG Joining ARG - GLU Joining GLU - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - VAL Joining VAL - GLU Joining GLU - MET Joining MET - LYS Joining LYS - GLU Joining GLU - LYS Joining LYS - LYS Joining LYS - ALA Joining ALA - ARG Joining ARG - VAL Joining VAL - GLU Joining GLU - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - HID Joining HID - ALA Joining ALA - THR Joining THR - ARG Joining ARG - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - GLU Joining GLU - GLU Joining GLU - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - ALA Joining ALA - SER Joining SER - LYS Joining LYS - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - GLN Joining GLN - ASN Joining ASN - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Joining ASP - GLN Joining GLN - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - LEU Joining LEU - ARG Joining ARG - ALA Joining ALA - MET Joining MET - GLU Joining GLU - ALA Joining ALA - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - GLN Joining GLN - ILE Joining ILE - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - CYS Joining CYS - GLY Joining GLY - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - ASN Joining ASN - THR Joining THR - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - TYR Joining TYR - ASN Joining ASN - ALA Joining ALA - ALA Joining ALA - THR Joining THR - GLU Joining GLU - GLU Joining GLU - TYR Joining TYR - GLY Joining GLY - ASN Joining ASN - MET Joining MET - ILE Joining ILE - ASP Joining ASP - MET Joining MET - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - THR Joining THR - LYS Joining LYS - VAL Joining VAL - THR Joining THR - ARG Joining ARG - SER Joining SER - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - TYR Joining TYR - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - ALA Joining ALA - GLY Joining GLY - LEU Joining LEU - MET Joining MET - ILE Joining ILE - THR Joining THR - THR Joining THR - GLU Joining GLU - CYS Joining CYS - MET Joining MET - VAL Joining VAL - THR Joining THR - ASP Joining ASP - LEU Joining LEU - CPRO Added missing heavy atom: .R.A total atoms in file: 3846 Leap added 3978 missing atoms according to residue templates: 5 Heavy 3973 H / lone pairs > > #w = loadpdb waters_with_hbond_after_min_sol.pdb > #mol = combine {mol w} > > saveamberparm mol 2C7E_chainA_noWAT.prmtop 2C7E_chainA_noWAT.inpcrd Checking Unit. WARNING: There is a bond of 4.940917 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 8.152534 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -19.000003 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. total 1366 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 CPRO 1 NALA 1 ) (no restraints) > > #solvateoct mol TIP3PBOX 16.0 0.78 > #saveamberparm mol 2C7E_chainA_sol.prmtop 2C7E_chainA_sol.inpcrd > quit Quit