log started: Thu Feb 17 16:26:56 2011 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/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: /opt/apps/amber/10/openmpi-mkl/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 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > mol = loadpdb pon1.pdb Loading PDB file: ./pon1.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: THR, Nonterminal, was not found in name map.) (Residue 5: ALA, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: MET, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: ALA, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: PHE, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: ARG, Nonterminal, was not found in name map.) (Residue 19: GLN, Nonterminal, was not found in name map.) (Residue 20: LYS, Nonterminal, was not found in name map.) (Residue 21: SER, Nonterminal, was not found in name map.) (Residue 22: SER, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: GLN, Nonterminal, was not found in name map.) (Residue 25: THR, Nonterminal, was not found in name map.) (Residue 26: ARG, Nonterminal, was not found in name map.) (Residue 27: PHE, Nonterminal, was not found in name map.) (Residue 28: ASN, Nonterminal, was not found in name map.) (Residue 29: VAL, Nonterminal, was not found in name map.) (Residue 30: HIE, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: GLU, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: ASN, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: ASN, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: LYS, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: ASN, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: SER, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: PRO, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: ALA, Nonterminal, was not found in name map.) (Residue 63: PHE, Nonterminal, was not found in name map.) (Residue 64: ILE, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: GLY, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: TYR, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: GLY, Nonterminal, was not found in name map.) (Residue 73: ILE, Nonterminal, was not found in name map.) (Residue 74: MET, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: PHE, Nonterminal, was not found in name map.) (Residue 77: ASP, Nonterminal, was not found in name map.) (Residue 78: PRO, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: LYS, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: LYS, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: LEU, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: MET, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: ASN, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: LYS, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: PRO, Nonterminal, was not found in name map.) (Residue 95: ALA, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: GLU, Nonterminal, was not found in name map.) (Residue 99: LEU, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: ILE, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: GLY, Nonterminal, was not found in name map.) (Residue 104: ASN, Nonterminal, was not found in name map.) (Residue 105: THR, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: ILE, Nonterminal, was not found in name map.) (Residue 109: SER, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PHE, Nonterminal, was not found in name map.) (Residue 112: ASN, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: HIE, Nonterminal, was not found in name map.) (Residue 115: GLY, Nonterminal, was not found in name map.) (Residue 116: ILE, Nonterminal, was not found in name map.) (Residue 117: SER, Nonterminal, was not found in name map.) (Residue 118: THR, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ASP, Nonterminal, was not found in name map.) (Residue 122: ASP, Nonterminal, was not found in name map.) (Residue 123: ASP, Nonterminal, was not found in name map.) (Residue 124: ASN, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: TYR, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: VAL, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIE, Nonterminal, was not found in name map.) (Residue 134: PRO, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: SER, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: SER, Nonterminal, was not found in name map.) (Residue 139: THR, Nonterminal, was not found in name map.) (Residue 140: VAL, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: PHE, Nonterminal, was not found in name map.) (Residue 144: LYS, Nonterminal, was not found in name map.) (Residue 145: PHE, Nonterminal, was not found in name map.) (Residue 146: GLN, Nonterminal, was not found in name map.) (Residue 147: GLU, Nonterminal, was not found in name map.) (Residue 148: GLU, Nonterminal, was not found in name map.) (Residue 149: GLU, Nonterminal, was not found in name map.) (Residue 150: LYS, Nonterminal, was not found in name map.) (Residue 151: SER, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: LEU, Nonterminal, was not found in name map.) (Residue 154: HIE, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: LYS, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: ILE, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: HIE, Nonterminal, was not found in name map.) (Residue 161: LYS, Nonterminal, was not found in name map.) (Residue 162: LEU, Nonterminal, was not found in name map.) (Residue 163: LEU, Nonterminal, was not found in name map.) (Residue 164: PRO, Nonterminal, was not found in name map.) (Residue 165: SER, Nonterminal, was not found in name map.) (Residue 166: VAL, Nonterminal, was not found in name map.) (Residue 167: ASN, Nonterminal, was not found in name map.) (Residue 168: ASP, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: ALA, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: GLY, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: GLU, Nonterminal, was not found in name map.) (Residue 176: HIE, Nonterminal, was not found in name map.) (Residue 177: PHE, Nonterminal, was not found in name map.) (Residue 178: TYR, Nonterminal, was not found in name map.) (Residue 179: ALA, Nonterminal, was not found in name map.) (Residue 180: THR, Nonterminal, was not found in name map.) (Residue 181: ASN, Nonterminal, was not found in name map.) (Residue 182: ASP, Nonterminal, was not found in name map.) (Residue 183: HIE, Nonterminal, was not found in name map.) (Residue 184: TYR, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: ASP, Nonterminal, was not found in name map.) (Residue 188: PRO, Nonterminal, was not found in name map.) (Residue 189: TYR, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: LYS, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLU, Nonterminal, was not found in name map.) (Residue 195: MET, Nonterminal, was not found in name map.) (Residue 196: HIE, Nonterminal, was not found in name map.) (Residue 197: LEU, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: ALA, Nonterminal, was not found in name map.) (Residue 201: TRP, Nonterminal, was not found in name map.) (Residue 202: SER, Nonterminal, was not found in name map.) (Residue 203: PHE, Nonterminal, was not found in name map.) (Residue 204: VAL, Nonterminal, was not found in name map.) (Residue 205: THR, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: SER, Nonterminal, was not found in name map.) (Residue 209: PRO, Nonterminal, was not found in name map.) (Residue 210: ASN, Nonterminal, was not found in name map.) (Residue 211: ASP, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: VAL, Nonterminal, was not found in name map.) (Residue 215: VAL, Nonterminal, was not found in name map.) (Residue 216: ALA, Nonterminal, was not found in name map.) (Residue 217: GLU, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: PHE, Nonterminal, was not found in name map.) (Residue 220: ASP, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: ALA, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: GLY, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ASN, Nonterminal, was not found in name map.) (Residue 227: ILE, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: PRO, Nonterminal, was not found in name map.) (Residue 230: ASP, Nonterminal, was not found in name map.) (Residue 231: GLY, Nonterminal, was not found in name map.) (Residue 232: LYS, Nonterminal, was not found in name map.) (Residue 233: TYR, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: TYR, Nonterminal, was not found in name map.) (Residue 236: ILE, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: GLU, Nonterminal, was not found in name map.) (Residue 239: LEU, Nonterminal, was not found in name map.) (Residue 240: LEU, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: HIE, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: ILE, Nonterminal, was not found in name map.) (Residue 245: HIE, Nonterminal, was not found in name map.) (Residue 246: VAL, Nonterminal, was not found in name map.) (Residue 247: TYR, Nonterminal, was not found in name map.) (Residue 248: GLU, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: HIE, Nonterminal, was not found in name map.) (Residue 251: ALA, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: TRP, Nonterminal, was not found in name map.) (Residue 254: THR, Nonterminal, was not found in name map.) (Residue 255: LEU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: LEU, Nonterminal, was not found in name map.) (Residue 259: ARG, Nonterminal, was not found in name map.) (Residue 260: VAL, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: SER, Nonterminal, was not found in name map.) (Residue 263: PHE, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: THR, Nonterminal, was not found in name map.) (Residue 266: LEU, Nonterminal, was not found in name map.) (Residue 267: VAL, Nonterminal, was not found in name map.) (Residue 268: ASP, Nonterminal, was not found in name map.) (Residue 269: ASN, Nonterminal, was not found in name map.) (Residue 270: ILE, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: VAL, Nonterminal, was not found in name map.) (Residue 273: ASP, Nonterminal, was not found in name map.) (Residue 274: PRO, Nonterminal, was not found in name map.) (Residue 275: VAL, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: GLY, Nonterminal, was not found in name map.) (Residue 278: ASP, Nonterminal, was not found in name map.) (Residue 279: LEU, Nonterminal, was not found in name map.) (Residue 280: TRP, Nonterminal, was not found in name map.) (Residue 281: VAL, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: CYS, Nonterminal, was not found in name map.) (Residue 284: HIE, Nonterminal, was not found in name map.) (Residue 285: PRO, Nonterminal, was not found in name map.) (Residue 286: ASN, Nonterminal, was not found in name map.) (Residue 287: GLY, Nonterminal, was not found in name map.) (Residue 288: MET, Nonterminal, was not found in name map.) (Residue 289: ARG, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: PHE, Nonterminal, was not found in name map.) (Residue 292: PHE, Nonterminal, was not found in name map.) (Residue 293: TYR, Nonterminal, was not found in name map.) (Residue 294: ASP, Nonterminal, was not found in name map.) (Residue 295: ALA, Nonterminal, was not found in name map.) (Residue 296: GLU, Nonterminal, was not found in name map.) (Residue 297: ASN, Nonterminal, was not found in name map.) (Residue 298: PRO, Nonterminal, was not found in name map.) (Residue 299: PRO, Nonterminal, was not found in name map.) (Residue 300: GLY, Nonterminal, was not found in name map.) (Residue 301: SER, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: VAL, Nonterminal, was not found in name map.) (Residue 304: LEU, Nonterminal, was not found in name map.) (Residue 305: ARG, Nonterminal, was not found in name map.) (Residue 306: ILE, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ILE, Nonterminal, was not found in name map.) (Residue 310: LEU, Nonterminal, was not found in name map.) (Residue 311: SER, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: PRO, Nonterminal, was not found in name map.) (Residue 315: LYS, Nonterminal, was not found in name map.) (Residue 316: VAL, Nonterminal, was not found in name map.) (Residue 317: THR, Nonterminal, was not found in name map.) (Residue 318: VAL, Nonterminal, was not found in name map.) (Residue 319: VAL, Nonterminal, was not found in name map.) (Residue 320: TYR, Nonterminal, was not found in name map.) (Residue 321: ALA, Nonterminal, was not found in name map.) (Residue 322: GLU, Nonterminal, was not found in name map.) (Residue 323: ASN, Nonterminal, was not found in name map.) (Residue 324: GLY, Nonterminal, was not found in name map.) (Residue 325: THR, Nonterminal, was not found in name map.) (Residue 326: VAL, Nonterminal, was not found in name map.) (Residue 327: LEU, Nonterminal, was not found in name map.) (Residue 328: GLN, Nonterminal, was not found in name map.) (Residue 329: GLY, Nonterminal, was not found in name map.) (Residue 330: SER, Nonterminal, was not found in name map.) (Residue 331: THR, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ALA, Nonterminal, was not found in name map.) (Residue 334: ALA, Nonterminal, was not found in name map.) (Residue 335: VAL, Nonterminal, was not found in name map.) (Residue 336: TYR, Nonterminal, was not found in name map.) (Residue 337: LYS, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: LYS, Nonterminal, was not found in name map.) (Residue 340: LEU, Nonterminal, was not found in name map.) (Residue 341: LEU, Nonterminal, was not found in name map.) (Residue 342: ILE, Nonterminal, was not found in name map.) (Residue 343: GLY, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: VAL, Nonterminal, was not found in name map.) (Residue 346: PHE, Nonterminal, was not found in name map.) (Residue 347: HIE, Nonterminal, was not found in name map.) (Residue 348: LYS, Nonterminal, was not found in name map.) (Residue 349: ALA, Nonterminal, was not found in name map.) (Residue 350: LEU, Nonterminal, was not found in name map.) (Residue 351: TYR, Nonterminal, was not found in name map.) (Residue 352: CYS, Nonterminal, was not found in name map.) (Residue 353: ASP, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 354 to: CLEU. (Residue 355: KA, Terminal/last, was not found in name map.) Unknown residue: KA number: 355 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining NMET - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - THR Joining THR - ALA Joining ALA - LEU Joining LEU - THR Joining THR - LEU Joining LEU - LEU Joining LEU - GLY Joining GLY - MET Joining MET - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLN Joining GLN - LYS Joining LYS - SER Joining SER - SER Joining SER - PHE Joining PHE - GLN Joining GLN - THR Joining THR - ARG Joining ARG - PHE Joining PHE - ASN Joining ASN - VAL Joining VAL - HIE Joining HIE - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - PRO Joining PRO - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - CYS Joining CYS - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - ASN Joining ASN - GLY Joining GLY - SER Joining SER - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - PHE Joining PHE - ILE Joining ILE - SER Joining SER - SER Joining SER - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - ILE Joining ILE - MET Joining MET - SER Joining SER - PHE Joining PHE - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - LYS Joining LYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ASP Joining ASP - LEU Joining LEU - ASN Joining ASN - GLU Joining GLU - LYS Joining LYS - GLU Joining GLU - PRO Joining PRO - ALA Joining ALA - VAL Joining VAL - SER Joining SER - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - ILE Joining ILE - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASP Joining ASP - ILE Joining ILE - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - PRO Joining PRO - HIE Joining HIE - GLY Joining GLY - ILE Joining ILE - SER Joining SER - THR Joining THR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - ASP Joining ASP - ASN Joining ASN - THR Joining THR - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - HIE Joining HIE - PRO Joining PRO - GLY Joining GLY - SER Joining SER - SER Joining SER - SER Joining SER - THR Joining THR - VAL Joining VAL - GLU Joining GLU - VAL Joining VAL - PHE Joining PHE - LYS Joining LYS - PHE Joining PHE - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - SER Joining SER - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - LEU Joining LEU - LYS Joining LYS - THR Joining THR - ILE Joining ILE - ARG Joining ARG - HIE Joining HIE - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - TYR Joining TYR - ALA Joining ALA - THR Joining THR - ASN Joining ASN - ASP Joining ASP - HIE Joining HIE - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - LEU Joining LEU - LYS Joining LYS - SER Joining SER - TRP Joining TRP - GLU Joining GLU - MET Joining MET - HIE Joining HIE - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - SER Joining SER - PHE Joining PHE - VAL Joining VAL - THR Joining THR - TYR Joining TYR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - ASN Joining ASN - ASP Joining ASP - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - ILE Joining ILE - ASN Joining ASN - ILE Joining ILE - SER Joining SER - PRO Joining PRO - ASP Joining ASP - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - VAL Joining VAL - TYR Joining TYR - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - HIE Joining HIE - LYS Joining LYS - ILE Joining ILE - HIE Joining HIE - VAL Joining VAL - TYR Joining TYR - GLU Joining GLU - LYS Joining LYS - HIE Joining HIE - ALA Joining ALA - ASN Joining ASN - TRP Joining TRP - THR Joining THR - LEU Joining LEU - THR Joining THR - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ASP Joining ASP - THR Joining THR - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - SER Joining SER - VAL Joining VAL - ASP Joining ASP - PRO Joining PRO - VAL Joining VAL - THR Joining THR - GLY Joining GLY - ASP Joining ASP - LEU Joining LEU - TRP Joining TRP - VAL Joining VAL - GLY Joining GLY - CYS Joining CYS - HIE Joining HIE - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - MET Joining MET - ARG Joining ARG - ILE Joining ILE - PHE Joining PHE - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - SER Joining SER - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - LEU Joining LEU - SER Joining SER - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - LYS Joining LYS - VAL Joining VAL - THR Joining THR - VAL Joining VAL - VAL Joining VAL - TYR Joining TYR - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - SER Joining SER - THR Joining THR - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - TYR Joining TYR - LYS Joining LYS - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - THR Joining THR - VAL Joining VAL - PHE Joining PHE - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - CYS Joining CYS - ASP Joining ASP - CLEU Creating new UNIT for residue: KA sequence: 356 Created a new atom named: KA within residue: .R total atoms in file: 2796 Leap added 2759 missing atoms according to residue templates: 2759 H / lone pairs The file contained 1 atoms not in residue templates log started: Fri Feb 18 10:31:08 2011 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CG" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /opt/apps/amber/10/openmpi-mkl/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: /opt/apps/amber/10/openmpi-mkl/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 > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } > { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } > { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } > { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } > { 0 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'1" } > { "H2*2" "H2'2" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > mol = loadpdb new.pdb Loading PDB file: ./new.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: THR, Nonterminal, was not found in name map.) (Residue 5: ALA, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: MET, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: ALA, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: PHE, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: ARG, Nonterminal, was not found in name map.) (Residue 19: GLN, Nonterminal, was not found in name map.) (Residue 20: LYS, Nonterminal, was not found in name map.) (Residue 21: SER, Nonterminal, was not found in name map.) (Residue 22: SER, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: GLN, Nonterminal, was not found in name map.) (Residue 25: THR, Nonterminal, was not found in name map.) (Residue 26: ARG, Nonterminal, was not found in name map.) (Residue 27: PHE, Nonterminal, was not found in name map.) (Residue 28: ASN, Nonterminal, was not found in name map.) (Residue 29: VAL, Nonterminal, was not found in name map.) (Residue 30: HIE, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: GLU, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: ASN, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: ASN, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: LYS, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: ASN, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: SER, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: PRO, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: ALA, Nonterminal, was not found in name map.) (Residue 63: PHE, Nonterminal, was not found in name map.) (Residue 64: ILE, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: GLY, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: TYR, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: GLY, Nonterminal, was not found in name map.) (Residue 73: ILE, Nonterminal, was not found in name map.) (Residue 74: MET, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: PHE, Nonterminal, was not found in name map.) (Residue 77: ASP, Nonterminal, was not found in name map.) (Residue 78: PRO, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: LYS, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: LYS, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: LEU, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: MET, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: ASN, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: LYS, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: PRO, Nonterminal, was not found in name map.) (Residue 95: ALA, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: GLU, Nonterminal, was not found in name map.) (Residue 99: LEU, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: ILE, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: GLY, Nonterminal, was not found in name map.) (Residue 104: ASN, Nonterminal, was not found in name map.) (Residue 105: THR, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: ILE, Nonterminal, was not found in name map.) (Residue 109: SER, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PHE, Nonterminal, was not found in name map.) (Residue 112: ASN, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: HIE, Nonterminal, was not found in name map.) (Residue 115: GLY, Nonterminal, was not found in name map.) (Residue 116: ILE, Nonterminal, was not found in name map.) (Residue 117: SER, Nonterminal, was not found in name map.) (Residue 118: THR, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ASP, Nonterminal, was not found in name map.) (Residue 122: ASP, Nonterminal, was not found in name map.) (Residue 123: ASP, Nonterminal, was not found in name map.) (Residue 124: ASN, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: TYR, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: VAL, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIE, Nonterminal, was not found in name map.) (Residue 134: PRO, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: SER, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: SER, Nonterminal, was not found in name map.) (Residue 139: THR, Nonterminal, was not found in name map.) (Residue 140: VAL, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: PHE, Nonterminal, was not found in name map.) (Residue 144: LYS, Nonterminal, was not found in name map.) (Residue 145: PHE, Nonterminal, was not found in name map.) (Residue 146: GLN, Nonterminal, was not found in name map.) (Residue 147: GLU, Nonterminal, was not found in name map.) (Residue 148: GLU, Nonterminal, was not found in name map.) (Residue 149: GLU, Nonterminal, was not found in name map.) (Residue 150: LYS, Nonterminal, was not found in name map.) (Residue 151: SER, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: LEU, Nonterminal, was not found in name map.) (Residue 154: HIE, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: LYS, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: ILE, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: HIE, Nonterminal, was not found in name map.) (Residue 161: LYS, Nonterminal, was not found in name map.) (Residue 162: LEU, Nonterminal, was not found in name map.) (Residue 163: LEU, Nonterminal, was not found in name map.) (Residue 164: PRO, Nonterminal, was not found in name map.) (Residue 165: SER, Nonterminal, was not found in name map.) (Residue 166: VAL, Nonterminal, was not found in name map.) (Residue 167: ASN, Nonterminal, was not found in name map.) (Residue 168: ASP, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: ALA, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: GLY, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: GLU, Nonterminal, was not found in name map.) (Residue 176: HIE, Nonterminal, was not found in name map.) (Residue 177: PHE, Nonterminal, was not found in name map.) (Residue 178: TYR, Nonterminal, was not found in name map.) (Residue 179: ALA, Nonterminal, was not found in name map.) (Residue 180: THR, Nonterminal, was not found in name map.) (Residue 181: ASN, Nonterminal, was not found in name map.) (Residue 182: ASP, Nonterminal, was not found in name map.) (Residue 183: HIE, Nonterminal, was not found in name map.) (Residue 184: TYR, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: ASP, Nonterminal, was not found in name map.) (Residue 188: PRO, Nonterminal, was not found in name map.) (Residue 189: TYR, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: LYS, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLU, Nonterminal, was not found in name map.) (Residue 195: MET, Nonterminal, was not found in name map.) (Residue 196: HIE, Nonterminal, was not found in name map.) (Residue 197: LEU, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: ALA, Nonterminal, was not found in name map.) (Residue 201: TRP, Nonterminal, was not found in name map.) (Residue 202: SER, Nonterminal, was not found in name map.) (Residue 203: PHE, Nonterminal, was not found in name map.) (Residue 204: VAL, Nonterminal, was not found in name map.) (Residue 205: THR, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: SER, Nonterminal, was not found in name map.) (Residue 209: PRO, Nonterminal, was not found in name map.) (Residue 210: ASN, Nonterminal, was not found in name map.) (Residue 211: ASP, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: VAL, Nonterminal, was not found in name map.) (Residue 215: VAL, Nonterminal, was not found in name map.) (Residue 216: ALA, Nonterminal, was not found in name map.) (Residue 217: GLU, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: PHE, Nonterminal, was not found in name map.) (Residue 220: ASP, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: ALA, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: GLY, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ASN, Nonterminal, was not found in name map.) (Residue 227: ILE, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: PRO, Nonterminal, was not found in name map.) (Residue 230: ASP, Nonterminal, was not found in name map.) (Residue 231: GLY, Nonterminal, was not found in name map.) (Residue 232: LYS, Nonterminal, was not found in name map.) (Residue 233: TYR, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: TYR, Nonterminal, was not found in name map.) (Residue 236: ILE, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: GLU, Nonterminal, was not found in name map.) (Residue 239: LEU, Nonterminal, was not found in name map.) (Residue 240: LEU, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: HIE, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: ILE, Nonterminal, was not found in name map.) (Residue 245: HIE, Nonterminal, was not found in name map.) (Residue 246: VAL, Nonterminal, was not found in name map.) (Residue 247: TYR, Nonterminal, was not found in name map.) (Residue 248: GLU, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: HIE, Nonterminal, was not found in name map.) (Residue 251: ALA, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: TRP, Nonterminal, was not found in name map.) (Residue 254: THR, Nonterminal, was not found in name map.) (Residue 255: LEU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: LEU, Nonterminal, was not found in name map.) (Residue 259: ARG, Nonterminal, was not found in name map.) (Residue 260: VAL, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: SER, Nonterminal, was not found in name map.) (Residue 263: PHE, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: THR, Nonterminal, was not found in name map.) (Residue 266: LEU, Nonterminal, was not found in name map.) (Residue 267: VAL, Nonterminal, was not found in name map.) (Residue 268: ASP, Nonterminal, was not found in name map.) (Residue 269: ASN, Nonterminal, was not found in name map.) (Residue 270: ILE, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: VAL, Nonterminal, was not found in name map.) (Residue 273: ASP, Nonterminal, was not found in name map.) (Residue 274: PRO, Nonterminal, was not found in name map.) (Residue 275: VAL, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: GLY, Nonterminal, was not found in name map.) (Residue 278: ASP, Nonterminal, was not found in name map.) (Residue 279: LEU, Nonterminal, was not found in name map.) (Residue 280: TRP, Nonterminal, was not found in name map.) (Residue 281: VAL, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: CYS, Nonterminal, was not found in name map.) (Residue 284: HIE, Nonterminal, was not found in name map.) (Residue 285: PRO, Nonterminal, was not found in name map.) (Residue 286: ASN, Nonterminal, was not found in name map.) (Residue 287: GLY, Nonterminal, was not found in name map.) (Residue 288: MET, Nonterminal, was not found in name map.) (Residue 289: ARG, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: PHE, Nonterminal, was not found in name map.) (Residue 292: PHE, Nonterminal, was not found in name map.) (Residue 293: TYR, Nonterminal, was not found in name map.) (Residue 294: ASP, Nonterminal, was not found in name map.) (Residue 295: ALA, Nonterminal, was not found in name map.) (Residue 296: GLU, Nonterminal, was not found in name map.) (Residue 297: ASN, Nonterminal, was not found in name map.) (Residue 298: PRO, Nonterminal, was not found in name map.) (Residue 299: PRO, Nonterminal, was not found in name map.) (Residue 300: GLY, Nonterminal, was not found in name map.) (Residue 301: SER, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: VAL, Nonterminal, was not found in name map.) (Residue 304: LEU, Nonterminal, was not found in name map.) (Residue 305: ARG, Nonterminal, was not found in name map.) (Residue 306: ILE, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ILE, Nonterminal, was not found in name map.) (Residue 310: LEU, Nonterminal, was not found in name map.) (Residue 311: SER, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: PRO, Nonterminal, was not found in name map.) (Residue 315: LYS, Nonterminal, was not found in name map.) (Residue 316: VAL, Nonterminal, was not found in name map.) (Residue 317: THR, Nonterminal, was not found in name map.) (Residue 318: VAL, Nonterminal, was not found in name map.) (Residue 319: VAL, Nonterminal, was not found in name map.) (Residue 320: TYR, Nonterminal, was not found in name map.) (Residue 321: ALA, Nonterminal, was not found in name map.) (Residue 322: GLU, Nonterminal, was not found in name map.) (Residue 323: ASN, Nonterminal, was not found in name map.) (Residue 324: GLY, Nonterminal, was not found in name map.) (Residue 325: THR, Nonterminal, was not found in name map.) (Residue 326: VAL, Nonterminal, was not found in name map.) (Residue 327: LEU, Nonterminal, was not found in name map.) (Residue 328: GLN, Nonterminal, was not found in name map.) (Residue 329: GLY, Nonterminal, was not found in name map.) (Residue 330: SER, Nonterminal, was not found in name map.) (Residue 331: THR, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ALA, Nonterminal, was not found in name map.) (Residue 334: ALA, Nonterminal, was not found in name map.) (Residue 335: VAL, Nonterminal, was not found in name map.) (Residue 336: TYR, Nonterminal, was not found in name map.) (Residue 337: LYS, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: LYS, Nonterminal, was not found in name map.) (Residue 340: LEU, Nonterminal, was not found in name map.) (Residue 341: LEU, Nonterminal, was not found in name map.) (Residue 342: ILE, Nonterminal, was not found in name map.) (Residue 343: GLY, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: VAL, Nonterminal, was not found in name map.) (Residue 346: PHE, Nonterminal, was not found in name map.) (Residue 347: HIE, Nonterminal, was not found in name map.) (Residue 348: LYS, Nonterminal, was not found in name map.) (Residue 349: ALA, Nonterminal, was not found in name map.) (Residue 350: LEU, Nonterminal, was not found in name map.) (Residue 351: TYR, Nonterminal, was not found in name map.) (Residue 352: CYS, Nonterminal, was not found in name map.) (Residue 353: ASP, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 354 to: CLEU. (Residue 355: CA, Terminal/last, was not found in name map.) Unknown residue: CA number: 355 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining NMET - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - THR Joining THR - ALA Joining ALA - LEU Joining LEU - THR Joining THR - LEU Joining LEU - LEU Joining LEU - GLY Joining GLY - MET Joining MET - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLN Joining GLN - LYS Joining LYS - SER Joining SER - SER Joining SER - PHE Joining PHE - GLN Joining GLN - THR Joining THR - ARG Joining ARG - PHE Joining PHE - ASN Joining ASN - VAL Joining VAL - HIE Joining HIE - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - PRO Joining PRO - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - CYS Joining CYS - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - ASN Joining ASN - GLY Joining GLY - SER Joining SER - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - PHE Joining PHE - ILE Joining ILE - SER Joining SER - SER Joining SER - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - ILE Joining ILE - MET Joining MET - SER Joining SER - PHE Joining PHE - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - LYS Joining LYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ASP Joining ASP - LEU Joining LEU - ASN Joining ASN - GLU Joining GLU - LYS Joining LYS - GLU Joining GLU - PRO Joining PRO - ALA Joining ALA - VAL Joining VAL - SER Joining SER - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - ILE Joining ILE - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASP Joining ASP - ILE Joining ILE - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - PRO Joining PRO - HIE Joining HIE - GLY Joining GLY - ILE Joining ILE - SER Joining SER - THR Joining THR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - ASP Joining ASP - ASN Joining ASN - THR Joining THR - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - HIE Joining HIE - PRO Joining PRO - GLY Joining GLY - SER Joining SER - SER Joining SER - SER Joining SER - THR Joining THR - VAL Joining VAL - GLU Joining GLU - VAL Joining VAL - PHE Joining PHE - LYS Joining LYS - PHE Joining PHE - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - SER Joining SER - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - LEU Joining LEU - LYS Joining LYS - THR Joining THR - ILE Joining ILE - ARG Joining ARG - HIE Joining HIE - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - TYR Joining TYR - ALA Joining ALA - THR Joining THR - ASN Joining ASN - ASP Joining ASP - HIE Joining HIE - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - LEU Joining LEU - LYS Joining LYS - SER Joining SER - TRP Joining TRP - GLU Joining GLU - MET Joining MET - HIE Joining HIE - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - SER Joining SER - PHE Joining PHE - VAL Joining VAL - THR Joining THR - TYR Joining TYR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - ASN Joining ASN - ASP Joining ASP - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - ILE Joining ILE - ASN Joining ASN - ILE Joining ILE - SER Joining SER - PRO Joining PRO - ASP Joining ASP - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - VAL Joining VAL - TYR Joining TYR - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - HIE Joining HIE - LYS Joining LYS - ILE Joining ILE - HIE Joining HIE - VAL Joining VAL - TYR Joining TYR - GLU Joining GLU - LYS Joining LYS - HIE Joining HIE - ALA Joining ALA - ASN Joining ASN - TRP Joining TRP - THR Joining THR - LEU Joining LEU - THR Joining THR - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ASP Joining ASP - THR Joining THR - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - SER Joining SER - VAL Joining VAL - ASP Joining ASP - PRO Joining PRO - VAL Joining VAL - THR Joining THR - GLY Joining GLY - ASP Joining ASP - LEU Joining LEU - TRP Joining TRP - VAL Joining VAL - GLY Joining GLY - CYS Joining CYS - HIE Joining HIE - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - MET Joining MET - ARG Joining ARG - ILE Joining ILE - PHE Joining PHE - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - SER Joining SER - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - LEU Joining LEU - SER Joining SER - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - LYS Joining LYS - VAL Joining VAL - THR Joining THR - VAL Joining VAL - VAL Joining VAL - TYR Joining TYR - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - SER Joining SER - THR Joining THR - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - TYR Joining TYR - LYS Joining LYS - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - THR Joining THR - VAL Joining VAL - PHE Joining PHE - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - CYS Joining CYS - ASP Joining ASP - CLEU Creating new UNIT for residue: CA sequence: 356 Created a new atom named: CA within residue: .R total atoms in file: 5555 The file contained 1 atoms not in residue templates > loadamberprep metals.prp Loading Prep file: ./metals.prp (UNKNOWN ATOM TYPE: KA) Loaded UNIT: CAL > mol = loadpdb new.pdb Loading PDB file: ./new.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: ALA, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: THR, Nonterminal, was not found in name map.) (Residue 5: ALA, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: LEU, Nonterminal, was not found in name map.) (Residue 10: GLY, Nonterminal, was not found in name map.) (Residue 11: MET, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: ALA, Nonterminal, was not found in name map.) (Residue 15: LEU, Nonterminal, was not found in name map.) (Residue 16: PHE, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: ARG, Nonterminal, was not found in name map.) (Residue 19: GLN, Nonterminal, was not found in name map.) (Residue 20: LYS, Nonterminal, was not found in name map.) (Residue 21: SER, Nonterminal, was not found in name map.) (Residue 22: SER, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: GLN, Nonterminal, was not found in name map.) (Residue 25: THR, Nonterminal, was not found in name map.) (Residue 26: ARG, Nonterminal, was not found in name map.) (Residue 27: PHE, Nonterminal, was not found in name map.) (Residue 28: ASN, Nonterminal, was not found in name map.) (Residue 29: VAL, Nonterminal, was not found in name map.) (Residue 30: HIE, Nonterminal, was not found in name map.) (Residue 31: ARG, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: VAL, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: VAL, Nonterminal, was not found in name map.) (Residue 37: GLU, Nonterminal, was not found in name map.) (Residue 38: LEU, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: ASN, Nonterminal, was not found in name map.) (Residue 41: CYS, Nonterminal, was not found in name map.) (Residue 42: ASN, Nonterminal, was not found in name map.) (Residue 43: LEU, Nonterminal, was not found in name map.) (Residue 44: VAL, Nonterminal, was not found in name map.) (Residue 45: LYS, Nonterminal, was not found in name map.) (Residue 46: GLY, Nonterminal, was not found in name map.) (Residue 47: ILE, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: ASN, Nonterminal, was not found in name map.) (Residue 50: GLY, Nonterminal, was not found in name map.) (Residue 51: SER, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: ASP, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: GLU, Nonterminal, was not found in name map.) (Residue 56: ILE, Nonterminal, was not found in name map.) (Residue 57: LEU, Nonterminal, was not found in name map.) (Residue 58: PRO, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) (Residue 60: GLY, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: ALA, Nonterminal, was not found in name map.) (Residue 63: PHE, Nonterminal, was not found in name map.) (Residue 64: ILE, Nonterminal, was not found in name map.) (Residue 65: SER, Nonterminal, was not found in name map.) (Residue 66: SER, Nonterminal, was not found in name map.) (Residue 67: GLY, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: LYS, Nonterminal, was not found in name map.) (Residue 70: TYR, Nonterminal, was not found in name map.) (Residue 71: PRO, Nonterminal, was not found in name map.) (Residue 72: GLY, Nonterminal, was not found in name map.) (Residue 73: ILE, Nonterminal, was not found in name map.) (Residue 74: MET, Nonterminal, was not found in name map.) (Residue 75: SER, Nonterminal, was not found in name map.) (Residue 76: PHE, Nonterminal, was not found in name map.) (Residue 77: ASP, Nonterminal, was not found in name map.) (Residue 78: PRO, Nonterminal, was not found in name map.) (Residue 79: ASP, Nonterminal, was not found in name map.) (Residue 80: LYS, Nonterminal, was not found in name map.) (Residue 81: SER, Nonterminal, was not found in name map.) (Residue 82: GLY, Nonterminal, was not found in name map.) (Residue 83: LYS, Nonterminal, was not found in name map.) (Residue 84: ILE, Nonterminal, was not found in name map.) (Residue 85: LEU, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: MET, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: ASN, Nonterminal, was not found in name map.) (Residue 91: GLU, Nonterminal, was not found in name map.) (Residue 92: LYS, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: PRO, Nonterminal, was not found in name map.) (Residue 95: ALA, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: SER, Nonterminal, was not found in name map.) (Residue 98: GLU, Nonterminal, was not found in name map.) (Residue 99: LEU, Nonterminal, was not found in name map.) (Residue 100: GLU, Nonterminal, was not found in name map.) (Residue 101: ILE, Nonterminal, was not found in name map.) (Residue 102: ILE, Nonterminal, was not found in name map.) (Residue 103: GLY, Nonterminal, was not found in name map.) (Residue 104: ASN, Nonterminal, was not found in name map.) (Residue 105: THR, Nonterminal, was not found in name map.) (Residue 106: LEU, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: ILE, Nonterminal, was not found in name map.) (Residue 109: SER, Nonterminal, was not found in name map.) (Residue 110: SER, Nonterminal, was not found in name map.) (Residue 111: PHE, Nonterminal, was not found in name map.) (Residue 112: ASN, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: HIE, Nonterminal, was not found in name map.) (Residue 115: GLY, Nonterminal, was not found in name map.) (Residue 116: ILE, Nonterminal, was not found in name map.) (Residue 117: SER, Nonterminal, was not found in name map.) (Residue 118: THR, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: ILE, Nonterminal, was not found in name map.) (Residue 121: ASP, Nonterminal, was not found in name map.) (Residue 122: ASP, Nonterminal, was not found in name map.) (Residue 123: ASP, Nonterminal, was not found in name map.) (Residue 124: ASN, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: VAL, Nonterminal, was not found in name map.) (Residue 127: TYR, Nonterminal, was not found in name map.) (Residue 128: LEU, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: VAL, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: HIE, Nonterminal, was not found in name map.) (Residue 134: PRO, Nonterminal, was not found in name map.) (Residue 135: GLY, Nonterminal, was not found in name map.) (Residue 136: SER, Nonterminal, was not found in name map.) (Residue 137: SER, Nonterminal, was not found in name map.) (Residue 138: SER, Nonterminal, was not found in name map.) (Residue 139: THR, Nonterminal, was not found in name map.) (Residue 140: VAL, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: VAL, Nonterminal, was not found in name map.) (Residue 143: PHE, Nonterminal, was not found in name map.) (Residue 144: LYS, Nonterminal, was not found in name map.) (Residue 145: PHE, Nonterminal, was not found in name map.) (Residue 146: GLN, Nonterminal, was not found in name map.) (Residue 147: GLU, Nonterminal, was not found in name map.) (Residue 148: GLU, Nonterminal, was not found in name map.) (Residue 149: GLU, Nonterminal, was not found in name map.) (Residue 150: LYS, Nonterminal, was not found in name map.) (Residue 151: SER, Nonterminal, was not found in name map.) (Residue 152: LEU, Nonterminal, was not found in name map.) (Residue 153: LEU, Nonterminal, was not found in name map.) (Residue 154: HIE, Nonterminal, was not found in name map.) (Residue 155: LEU, Nonterminal, was not found in name map.) (Residue 156: LYS, Nonterminal, was not found in name map.) (Residue 157: THR, Nonterminal, was not found in name map.) (Residue 158: ILE, Nonterminal, was not found in name map.) (Residue 159: ARG, Nonterminal, was not found in name map.) (Residue 160: HIE, Nonterminal, was not found in name map.) (Residue 161: LYS, Nonterminal, was not found in name map.) (Residue 162: LEU, Nonterminal, was not found in name map.) (Residue 163: LEU, Nonterminal, was not found in name map.) (Residue 164: PRO, Nonterminal, was not found in name map.) (Residue 165: SER, Nonterminal, was not found in name map.) (Residue 166: VAL, Nonterminal, was not found in name map.) (Residue 167: ASN, Nonterminal, was not found in name map.) (Residue 168: ASP, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: ALA, Nonterminal, was not found in name map.) (Residue 172: VAL, Nonterminal, was not found in name map.) (Residue 173: GLY, Nonterminal, was not found in name map.) (Residue 174: PRO, Nonterminal, was not found in name map.) (Residue 175: GLU, Nonterminal, was not found in name map.) (Residue 176: HIE, Nonterminal, was not found in name map.) (Residue 177: PHE, Nonterminal, was not found in name map.) (Residue 178: TYR, Nonterminal, was not found in name map.) (Residue 179: ALA, Nonterminal, was not found in name map.) (Residue 180: THR, Nonterminal, was not found in name map.) (Residue 181: ASN, Nonterminal, was not found in name map.) (Residue 182: ASP, Nonterminal, was not found in name map.) (Residue 183: HIE, Nonterminal, was not found in name map.) (Residue 184: TYR, Nonterminal, was not found in name map.) (Residue 185: PHE, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: ASP, Nonterminal, was not found in name map.) (Residue 188: PRO, Nonterminal, was not found in name map.) (Residue 189: TYR, Nonterminal, was not found in name map.) (Residue 190: LEU, Nonterminal, was not found in name map.) (Residue 191: LYS, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: TRP, Nonterminal, was not found in name map.) (Residue 194: GLU, Nonterminal, was not found in name map.) (Residue 195: MET, Nonterminal, was not found in name map.) (Residue 196: HIE, Nonterminal, was not found in name map.) (Residue 197: LEU, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: ALA, Nonterminal, was not found in name map.) (Residue 201: TRP, Nonterminal, was not found in name map.) (Residue 202: SER, Nonterminal, was not found in name map.) (Residue 203: PHE, Nonterminal, was not found in name map.) (Residue 204: VAL, Nonterminal, was not found in name map.) (Residue 205: THR, Nonterminal, was not found in name map.) (Residue 206: TYR, Nonterminal, was not found in name map.) (Residue 207: TYR, Nonterminal, was not found in name map.) (Residue 208: SER, Nonterminal, was not found in name map.) (Residue 209: PRO, Nonterminal, was not found in name map.) (Residue 210: ASN, Nonterminal, was not found in name map.) (Residue 211: ASP, Nonterminal, was not found in name map.) (Residue 212: VAL, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: VAL, Nonterminal, was not found in name map.) (Residue 215: VAL, Nonterminal, was not found in name map.) (Residue 216: ALA, Nonterminal, was not found in name map.) (Residue 217: GLU, Nonterminal, was not found in name map.) (Residue 218: GLY, Nonterminal, was not found in name map.) (Residue 219: PHE, Nonterminal, was not found in name map.) (Residue 220: ASP, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: ALA, Nonterminal, was not found in name map.) (Residue 223: ASN, Nonterminal, was not found in name map.) (Residue 224: GLY, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ASN, Nonterminal, was not found in name map.) (Residue 227: ILE, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: PRO, Nonterminal, was not found in name map.) (Residue 230: ASP, Nonterminal, was not found in name map.) (Residue 231: GLY, Nonterminal, was not found in name map.) (Residue 232: LYS, Nonterminal, was not found in name map.) (Residue 233: TYR, Nonterminal, was not found in name map.) (Residue 234: VAL, Nonterminal, was not found in name map.) (Residue 235: TYR, Nonterminal, was not found in name map.) (Residue 236: ILE, Nonterminal, was not found in name map.) (Residue 237: ALA, Nonterminal, was not found in name map.) (Residue 238: GLU, Nonterminal, was not found in name map.) (Residue 239: LEU, Nonterminal, was not found in name map.) (Residue 240: LEU, Nonterminal, was not found in name map.) (Residue 241: ALA, Nonterminal, was not found in name map.) (Residue 242: HIE, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: ILE, Nonterminal, was not found in name map.) (Residue 245: HIE, Nonterminal, was not found in name map.) (Residue 246: VAL, Nonterminal, was not found in name map.) (Residue 247: TYR, Nonterminal, was not found in name map.) (Residue 248: GLU, Nonterminal, was not found in name map.) (Residue 249: LYS, Nonterminal, was not found in name map.) (Residue 250: HIE, Nonterminal, was not found in name map.) (Residue 251: ALA, Nonterminal, was not found in name map.) (Residue 252: ASN, Nonterminal, was not found in name map.) (Residue 253: TRP, Nonterminal, was not found in name map.) (Residue 254: THR, Nonterminal, was not found in name map.) (Residue 255: LEU, Nonterminal, was not found in name map.) (Residue 256: THR, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: LEU, Nonterminal, was not found in name map.) (Residue 259: ARG, Nonterminal, was not found in name map.) (Residue 260: VAL, Nonterminal, was not found in name map.) (Residue 261: LEU, Nonterminal, was not found in name map.) (Residue 262: SER, Nonterminal, was not found in name map.) (Residue 263: PHE, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: THR, Nonterminal, was not found in name map.) (Residue 266: LEU, Nonterminal, was not found in name map.) (Residue 267: VAL, Nonterminal, was not found in name map.) (Residue 268: ASP, Nonterminal, was not found in name map.) (Residue 269: ASN, Nonterminal, was not found in name map.) (Residue 270: ILE, Nonterminal, was not found in name map.) (Residue 271: SER, Nonterminal, was not found in name map.) (Residue 272: VAL, Nonterminal, was not found in name map.) (Residue 273: ASP, Nonterminal, was not found in name map.) (Residue 274: PRO, Nonterminal, was not found in name map.) (Residue 275: VAL, Nonterminal, was not found in name map.) (Residue 276: THR, Nonterminal, was not found in name map.) (Residue 277: GLY, Nonterminal, was not found in name map.) (Residue 278: ASP, Nonterminal, was not found in name map.) (Residue 279: LEU, Nonterminal, was not found in name map.) (Residue 280: TRP, Nonterminal, was not found in name map.) (Residue 281: VAL, Nonterminal, was not found in name map.) (Residue 282: GLY, Nonterminal, was not found in name map.) (Residue 283: CYS, Nonterminal, was not found in name map.) (Residue 284: HIE, Nonterminal, was not found in name map.) (Residue 285: PRO, Nonterminal, was not found in name map.) (Residue 286: ASN, Nonterminal, was not found in name map.) (Residue 287: GLY, Nonterminal, was not found in name map.) (Residue 288: MET, Nonterminal, was not found in name map.) (Residue 289: ARG, Nonterminal, was not found in name map.) (Residue 290: ILE, Nonterminal, was not found in name map.) (Residue 291: PHE, Nonterminal, was not found in name map.) (Residue 292: PHE, Nonterminal, was not found in name map.) (Residue 293: TYR, Nonterminal, was not found in name map.) (Residue 294: ASP, Nonterminal, was not found in name map.) (Residue 295: ALA, Nonterminal, was not found in name map.) (Residue 296: GLU, Nonterminal, was not found in name map.) (Residue 297: ASN, Nonterminal, was not found in name map.) (Residue 298: PRO, Nonterminal, was not found in name map.) (Residue 299: PRO, Nonterminal, was not found in name map.) (Residue 300: GLY, Nonterminal, was not found in name map.) (Residue 301: SER, Nonterminal, was not found in name map.) (Residue 302: GLU, Nonterminal, was not found in name map.) (Residue 303: VAL, Nonterminal, was not found in name map.) (Residue 304: LEU, Nonterminal, was not found in name map.) (Residue 305: ARG, Nonterminal, was not found in name map.) (Residue 306: ILE, Nonterminal, was not found in name map.) (Residue 307: GLN, Nonterminal, was not found in name map.) (Residue 308: ASP, Nonterminal, was not found in name map.) (Residue 309: ILE, Nonterminal, was not found in name map.) (Residue 310: LEU, Nonterminal, was not found in name map.) (Residue 311: SER, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: GLU, Nonterminal, was not found in name map.) (Residue 314: PRO, Nonterminal, was not found in name map.) (Residue 315: LYS, Nonterminal, was not found in name map.) (Residue 316: VAL, Nonterminal, was not found in name map.) (Residue 317: THR, Nonterminal, was not found in name map.) (Residue 318: VAL, Nonterminal, was not found in name map.) (Residue 319: VAL, Nonterminal, was not found in name map.) (Residue 320: TYR, Nonterminal, was not found in name map.) (Residue 321: ALA, Nonterminal, was not found in name map.) (Residue 322: GLU, Nonterminal, was not found in name map.) (Residue 323: ASN, Nonterminal, was not found in name map.) (Residue 324: GLY, Nonterminal, was not found in name map.) (Residue 325: THR, Nonterminal, was not found in name map.) (Residue 326: VAL, Nonterminal, was not found in name map.) (Residue 327: LEU, Nonterminal, was not found in name map.) (Residue 328: GLN, Nonterminal, was not found in name map.) (Residue 329: GLY, Nonterminal, was not found in name map.) (Residue 330: SER, Nonterminal, was not found in name map.) (Residue 331: THR, Nonterminal, was not found in name map.) (Residue 332: VAL, Nonterminal, was not found in name map.) (Residue 333: ALA, Nonterminal, was not found in name map.) (Residue 334: ALA, Nonterminal, was not found in name map.) (Residue 335: VAL, Nonterminal, was not found in name map.) (Residue 336: TYR, Nonterminal, was not found in name map.) (Residue 337: LYS, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: LYS, Nonterminal, was not found in name map.) (Residue 340: LEU, Nonterminal, was not found in name map.) (Residue 341: LEU, Nonterminal, was not found in name map.) (Residue 342: ILE, Nonterminal, was not found in name map.) (Residue 343: GLY, Nonterminal, was not found in name map.) (Residue 344: THR, Nonterminal, was not found in name map.) (Residue 345: VAL, Nonterminal, was not found in name map.) (Residue 346: PHE, Nonterminal, was not found in name map.) (Residue 347: HIE, Nonterminal, was not found in name map.) (Residue 348: LYS, Nonterminal, was not found in name map.) (Residue 349: ALA, Nonterminal, was not found in name map.) (Residue 350: LEU, Nonterminal, was not found in name map.) (Residue 351: TYR, Nonterminal, was not found in name map.) (Residue 352: CYS, Nonterminal, was not found in name map.) (Residue 353: ASP, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 354 to: CLEU. (Residue 355: CA, Terminal/last, was not found in name map.) Unknown residue: CA number: 355 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining NMET - ALA Joining ALA - LYS Joining LYS - LEU Joining LEU - THR Joining THR - ALA Joining ALA - LEU Joining LEU - THR Joining THR - LEU Joining LEU - LEU Joining LEU - GLY Joining GLY - MET Joining MET - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PHE Joining PHE - ASP Joining ASP - ARG Joining ARG - GLN Joining GLN - LYS Joining LYS - SER Joining SER - SER Joining SER - PHE Joining PHE - GLN Joining GLN - THR Joining THR - ARG Joining ARG - PHE Joining PHE - ASN Joining ASN - VAL Joining VAL - HIE Joining HIE - ARG Joining ARG - GLU Joining GLU - VAL Joining VAL - THR Joining THR - PRO Joining PRO - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - CYS Joining CYS - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - ASN Joining ASN - GLY Joining GLY - SER Joining SER - GLU Joining GLU - ASP Joining ASP - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - PHE Joining PHE - ILE Joining ILE - SER Joining SER - SER Joining SER - GLY Joining GLY - LEU Joining LEU - LYS Joining LYS - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - ILE Joining ILE - MET Joining MET - SER Joining SER - PHE Joining PHE - ASP Joining ASP - PRO Joining PRO - ASP Joining ASP - LYS Joining LYS - SER Joining SER - GLY Joining GLY - LYS Joining LYS - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - MET Joining MET - ASP Joining ASP - LEU Joining LEU - ASN Joining ASN - GLU Joining GLU - LYS Joining LYS - GLU Joining GLU - PRO Joining PRO - ALA Joining ALA - VAL Joining VAL - SER Joining SER - GLU Joining GLU - LEU Joining LEU - GLU Joining GLU - ILE Joining ILE - ILE Joining ILE - GLY Joining GLY - ASN Joining ASN - THR Joining THR - LEU Joining LEU - ASP Joining ASP - ILE Joining ILE - SER Joining SER - SER Joining SER - PHE Joining PHE - ASN Joining ASN - PRO Joining PRO - HIE Joining HIE - GLY Joining GLY - ILE Joining ILE - SER Joining SER - THR Joining THR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - ASP Joining ASP - ASN Joining ASN - THR Joining THR - VAL Joining VAL - TYR Joining TYR - LEU Joining LEU - LEU Joining LEU - VAL Joining VAL - VAL Joining VAL - ASN Joining ASN - HIE Joining HIE - PRO Joining PRO - GLY Joining GLY - SER Joining SER - SER Joining SER - SER Joining SER - THR Joining THR - VAL Joining VAL - GLU Joining GLU - VAL Joining VAL - PHE Joining PHE - LYS Joining LYS - PHE Joining PHE - GLN Joining GLN - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - SER Joining SER - LEU Joining LEU - LEU Joining LEU - HIE Joining HIE - LEU Joining LEU - LYS Joining LYS - THR Joining THR - ILE Joining ILE - ARG Joining ARG - HIE Joining HIE - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - SER Joining SER - VAL Joining VAL - ASN Joining ASN - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - ALA Joining ALA - VAL Joining VAL - GLY Joining GLY - PRO Joining PRO - GLU Joining GLU - HIE Joining HIE - PHE Joining PHE - TYR Joining TYR - ALA Joining ALA - THR Joining THR - ASN Joining ASN - ASP Joining ASP - HIE Joining HIE - TYR Joining TYR - PHE Joining PHE - ILE Joining ILE - ASP Joining ASP - PRO Joining PRO - TYR Joining TYR - LEU Joining LEU - LYS Joining LYS - SER Joining SER - TRP Joining TRP - GLU Joining GLU - MET Joining MET - HIE Joining HIE - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - TRP Joining TRP - SER Joining SER - PHE Joining PHE - VAL Joining VAL - THR Joining THR - TYR Joining TYR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - ASN Joining ASN - ASP Joining ASP - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - VAL Joining VAL - ALA Joining ALA - GLU Joining GLU - GLY Joining GLY - PHE Joining PHE - ASP Joining ASP - PHE Joining PHE - ALA Joining ALA - ASN Joining ASN - GLY Joining GLY - ILE Joining ILE - ASN Joining ASN - ILE Joining ILE - SER Joining SER - PRO Joining PRO - ASP Joining ASP - GLY Joining GLY - LYS Joining LYS - TYR Joining TYR - VAL Joining VAL - TYR Joining TYR - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - HIE Joining HIE - LYS Joining LYS - ILE Joining ILE - HIE Joining HIE - VAL Joining VAL - TYR Joining TYR - GLU Joining GLU - LYS Joining LYS - HIE Joining HIE - ALA Joining ALA - ASN Joining ASN - TRP Joining TRP - THR Joining THR - LEU Joining LEU - THR Joining THR - PRO Joining PRO - LEU Joining LEU - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - SER Joining SER - PHE Joining PHE - ASP Joining ASP - THR Joining THR - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - ASN Joining ASN - ILE Joining ILE - SER Joining SER - VAL Joining VAL - ASP Joining ASP - PRO Joining PRO - VAL Joining VAL - THR Joining THR - GLY Joining GLY - ASP Joining ASP - LEU Joining LEU - TRP Joining TRP - VAL Joining VAL - GLY Joining GLY - CYS Joining CYS - HIE Joining HIE - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - MET Joining MET - ARG Joining ARG - ILE Joining ILE - PHE Joining PHE - PHE Joining PHE - TYR Joining TYR - ASP Joining ASP - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - SER Joining SER - GLU Joining GLU - VAL Joining VAL - LEU Joining LEU - ARG Joining ARG - ILE Joining ILE - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - LEU Joining LEU - SER Joining SER - GLU Joining GLU - GLU Joining GLU - PRO Joining PRO - LYS Joining LYS - VAL Joining VAL - THR Joining THR - VAL Joining VAL - VAL Joining VAL - TYR Joining TYR - ALA Joining ALA - GLU Joining GLU - ASN Joining ASN - GLY Joining GLY - THR Joining THR - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - SER Joining SER - THR Joining THR - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - VAL Joining VAL - TYR Joining TYR - LYS Joining LYS - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - ILE Joining ILE - GLY Joining GLY - THR Joining THR - VAL Joining VAL - PHE Joining PHE - HIE Joining HIE - LYS Joining LYS - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - CYS Joining CYS - ASP Joining ASP - CLEU Creating new UNIT for residue: CA sequence: 356 Created a new atom named: CA within residue: .R total atoms in file: 5555 The file contained 1 atoms not in residue templates