log started: Thu Jul 7 18:16:21 2011 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > # Load forcefield parameters > source leaprc.ff99SBildn ----- Source: /Users/jchodera/local/src/amber11/dat/leap/cmd/leaprc.ff99SBildn ----- Source of /Users/jchodera/local/src/amber11/dat/leap/cmd/leaprc.ff99SBildn done >> logFile leap.log log started: Thu Jul 7 18:16:21 2011 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # modified for the "ILDN" changes >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> #ildn >> { "C3" "C" "sp3" } >> { "C4" "C" "sp3" } >> { "C5" "C" "sp2" } >> { "C6" "C" "sp2" } >> { "NP" "N" "sp2" } >> { "OM" "O" "sp2" } # guess!!! >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: 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) >> mods = loadamberparams frcmod.ff99SBildn Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/frcmod.ff99SBildn Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) + ILDN corrections >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries (i.e. ff94 libs) >> # >> loadOff all_amino94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_amino94ildn.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_aminoct94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_aminoct94ildn.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_aminont94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_aminont94ildn.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: /Users/jchodera/local/src/amber11/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "O2*" "O2'" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > # Load additional ion parameters > #loadoff additional_ions.lib > #addPdbResMap { { 0 "Ca+" "Ca+" } { 1 "Ca+" "Ca+" } } > > # Load protein. > protein = loadpdb 1Y57.modelled.pdb Loading PDB file: ./1Y57.modelled.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. (Residue 1: ASN, Nonterminal, was not found in name map.) (Residue 2: ILE, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: ASN, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: CYS, Nonterminal, was not found in name map.) (Residue 11: LYS, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: ALA, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: PHE, Nonterminal, was not found in name map.) (Residue 16: GLY, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: ALA, Nonterminal, was not found in name map.) (Residue 19: ARG, Nonterminal, was not found in name map.) (Residue 20: LEU, Nonterminal, was not found in name map.) (Residue 21: ILE, Nonterminal, was not found in name map.) (Residue 22: GLU, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ASN, Nonterminal, was not found in name map.) (Residue 25: GLU, Nonterminal, was not found in name map.) (Residue 26: TYR, Nonterminal, was not found in name map.) (Residue 27: THR, Nonterminal, was not found in name map.) (Residue 28: ALA, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: GLN, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: ALA, Nonterminal, was not found in name map.) (Residue 33: LYS, Nonterminal, was not found in name map.) (Residue 34: PHE, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: ILE, Nonterminal, was not found in name map.) (Residue 37: LYS, Nonterminal, was not found in name map.) (Residue 38: TRP, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: PRO, Nonterminal, was not found in name map.) (Residue 42: GLU, Nonterminal, was not found in name map.) (Residue 43: ALA, Nonterminal, was not found in name map.) (Residue 44: ALA, Nonterminal, was not found in name map.) (Residue 45: LEU, Nonterminal, was not found in name map.) (Residue 46: TYR, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: ARG, Nonterminal, was not found in name map.) (Residue 49: PHE, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: ILE, Nonterminal, was not found in name map.) (Residue 52: LYS, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: ASP, Nonterminal, was not found in name map.) (Residue 55: VAL, Nonterminal, was not found in name map.) (Residue 56: TRP, Nonterminal, was not found in name map.) (Residue 57: SER, Nonterminal, was not found in name map.) (Residue 58: PHE, Nonterminal, was not found in name map.) (Residue 59: GLY, Nonterminal, was not found in name map.) (Residue 60: ILE, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: THR, Nonterminal, was not found in name map.) (Residue 64: GLU, Nonterminal, was not found in name map.) (Residue 65: LEU, Nonterminal, was not found in name map.) (Residue 66: THR, Nonterminal, was not found in name map.) (Residue 67: THR, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: ARG, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: PRO, Nonterminal, was not found in name map.) (Residue 73: TYR, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: GLY, Nonterminal, was not found in name map.) (Residue 76: MET, Nonterminal, was not found in name map.) (Residue 77: VAL, Nonterminal, was not found in name map.) (Residue 78: ASN, Nonterminal, was not found in name map.) (Residue 79: ARG, Nonterminal, was not found in name map.) (Residue 80: GLU, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: LEU, Nonterminal, was not found in name map.) (Residue 83: ASP, Nonterminal, was not found in name map.) (Residue 84: GLN, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: GLU, Nonterminal, was not found in name map.) (Residue 87: ARG, Nonterminal, was not found in name map.) (Residue 88: GLY, Nonterminal, was not found in name map.) (Residue 89: TYR, Nonterminal, was not found in name map.) (Residue 90: ARG, Nonterminal, was not found in name map.) (Residue 91: MET, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: CYS, Nonterminal, was not found in name map.) (Residue 94: PRO, Nonterminal, was not found in name map.) (Residue 95: PRO, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: CYS, Nonterminal, was not found in name map.) (Residue 98: PRO, Nonterminal, was not found in name map.) (Residue 99: GLU, Nonterminal, was not found in name map.) (Residue 100: SER, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: HIS, Nonterminal, was not found in name map.) (Residue 103: ASP, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: MET, Nonterminal, was not found in name map.) (Residue 106: CYS, Nonterminal, was not found in name map.) (Residue 107: GLN, Nonterminal, was not found in name map.) (Residue 108: CYS, Nonterminal, was not found in name map.) (Residue 109: TRP, Nonterminal, was not found in name map.) (Residue 110: ARG, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: GLU, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: GLU, Nonterminal, was not found in name map.) (Residue 115: GLU, Nonterminal, was not found in name map.) (Residue 116: ARG, Nonterminal, was not found in name map.) (Residue 117: PRO, 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: GLU, Nonterminal, was not found in name map.) (Residue 121: TYR, Nonterminal, was not found in name map.) (Residue 122: LEU, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: PHE, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: ASP, Nonterminal, was not found in name map.) (Residue 129: TYR, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: THR, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: THR, Nonterminal, was not found in name map.) (Residue 134: GLU, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: GLN, Nonterminal, was not found in name map.) (Residue 137: TYR, Nonterminal, was not found in name map.) (Residue 138: GLN, Nonterminal, was not found in name map.) (Residue 139: PRO, Nonterminal, was not found in name map.) (Residue 140: GLY, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 143 to: CLEU. Joining NALA - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - GLU Joining GLU - TYR Joining TYR - THR Joining THR - ALA Joining ALA - ARG Joining ARG - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - LYS Joining LYS - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - LYS Joining LYS - TRP Joining TRP - THR Joining THR - ALA Joining ALA - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - GLY Joining GLY - ARG Joining ARG - PHE Joining PHE - THR Joining THR - ILE Joining ILE - LYS Joining LYS - SER Joining SER - ASP Joining ASP - VAL Joining VAL - TRP Joining TRP - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - LEU Joining LEU - THR Joining THR - THR Joining THR - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - MET Joining MET - VAL Joining VAL - ASN Joining ASN - ARG Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ARG - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - VAL Joining VAL - LEU Joining LEU - ASP Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ASP - GLN Joining GLN - VAL Joining VAL - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - ARG Joining ARG - MET Joining MET - PRO Joining PRO - CYS Joining CYS - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - CYS Joining CYS - PRO Joining PRO - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - SER Joining SER - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - LEU Joining LEU - MET Joining MET - CYS Joining CYS - GLN Joining GLN - CYS Joining CYS - TRP Joining TRP - ARG Joining ARG - LYS Joining LYS - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - PRO Joining PRO - THR Joining THR - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - TYR Joining TYR - PHE Joining PHE - THR Joining THR - SER Joining SER - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLN Joining GLN - TYR Joining TYR - GLN Joining GLN - PRO Joining PRO - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - CLEU total atoms in file: 1148 Leap added 1149 missing atoms according to residue templates: 19 Heavy 1130 H / lone pairs > > logfile leapante.log log started: Thu Jul 7 18:17:17 2011 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > # Load forcefield parameters > source leaprc.ff99SBildn ----- Source: /Users/jchodera/local/src/amber11/dat/leap/cmd/leaprc.ff99SBildn ----- Source of /Users/jchodera/local/src/amber11/dat/leap/cmd/leaprc.ff99SBildn done >> logFile leap.log log started: Thu Jul 7 18:17:17 2011 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # modified for the "ILDN" changes >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> #ildn >> { "C3" "C" "sp3" } >> { "C4" "C" "sp3" } >> { "C5" "C" "sp2" } >> { "C6" "C" "sp2" } >> { "NP" "N" "sp2" } >> { "OM" "O" "sp2" } # guess!!! >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: 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) >> mods = loadamberparams frcmod.ff99SBildn Loading parameters: /Users/jchodera/local/src/amber11/dat/leap/parm/frcmod.ff99SBildn Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) + ILDN corrections >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries (i.e. ff94 libs) >> # >> loadOff all_amino94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_amino94ildn.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_aminoct94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_aminoct94ildn.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_aminont94ildn.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/all_aminont94ildn.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: /Users/jchodera/local/src/amber11/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /Users/jchodera/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "O2*" "O2'" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > # Load additional ion parameters > #loadoff additional_ions.lib > #addPdbResMap { { 0 "Ca+" "Ca+" } { 1 "Ca+" "Ca+" } } > > # Load protein. > protein = loadpdb 1Y57.modelled.pdb Loading PDB file: ./1Y57.modelled.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA. (Residue 1: ASN, Nonterminal, was not found in name map.) (Residue 2: ILE, Nonterminal, was not found in name map.) (Residue 3: LEU, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: GLY, Nonterminal, was not found in name map.) (Residue 6: GLU, Nonterminal, was not found in name map.) (Residue 7: ASN, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: CYS, Nonterminal, was not found in name map.) (Residue 11: LYS, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: ALA, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: PHE, Nonterminal, was not found in name map.) (Residue 16: GLY, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: ALA, Nonterminal, was not found in name map.) (Residue 19: ARG, Nonterminal, was not found in name map.) (Residue 20: LEU, Nonterminal, was not found in name map.) (Residue 21: ILE, Nonterminal, was not found in name map.) (Residue 22: GLU, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ASN, Nonterminal, was not found in name map.) (Residue 25: GLU, Nonterminal, was not found in name map.) (Residue 26: TYR, Nonterminal, was not found in name map.) (Residue 27: THR, Nonterminal, was not found in name map.) (Residue 28: ALA, Nonterminal, was not found in name map.) (Residue 29: ARG, Nonterminal, was not found in name map.) (Residue 30: GLN, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: ALA, Nonterminal, was not found in name map.) (Residue 33: LYS, Nonterminal, was not found in name map.) (Residue 34: PHE, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: ILE, Nonterminal, was not found in name map.) (Residue 37: LYS, Nonterminal, was not found in name map.) (Residue 38: TRP, Nonterminal, was not found in name map.) (Residue 39: THR, Nonterminal, was not found in name map.) (Residue 40: ALA, Nonterminal, was not found in name map.) (Residue 41: PRO, Nonterminal, was not found in name map.) (Residue 42: GLU, Nonterminal, was not found in name map.) (Residue 43: ALA, Nonterminal, was not found in name map.) (Residue 44: ALA, Nonterminal, was not found in name map.) (Residue 45: LEU, Nonterminal, was not found in name map.) (Residue 46: TYR, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: ARG, Nonterminal, was not found in name map.) (Residue 49: PHE, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: ILE, Nonterminal, was not found in name map.) (Residue 52: LYS, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: ASP, Nonterminal, was not found in name map.) (Residue 55: VAL, Nonterminal, was not found in name map.) (Residue 56: TRP, Nonterminal, was not found in name map.) (Residue 57: SER, Nonterminal, was not found in name map.) (Residue 58: PHE, Nonterminal, was not found in name map.) (Residue 59: GLY, Nonterminal, was not found in name map.) (Residue 60: ILE, Nonterminal, was not found in name map.) (Residue 61: LEU, Nonterminal, was not found in name map.) (Residue 62: LEU, Nonterminal, was not found in name map.) (Residue 63: THR, Nonterminal, was not found in name map.) (Residue 64: GLU, Nonterminal, was not found in name map.) (Residue 65: LEU, Nonterminal, was not found in name map.) (Residue 66: THR, Nonterminal, was not found in name map.) (Residue 67: THR, Nonterminal, was not found in name map.) (Residue 68: LYS, Nonterminal, was not found in name map.) (Residue 69: GLY, Nonterminal, was not found in name map.) (Residue 70: ARG, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: PRO, Nonterminal, was not found in name map.) (Residue 73: TYR, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: GLY, Nonterminal, was not found in name map.) (Residue 76: MET, Nonterminal, was not found in name map.) (Residue 77: VAL, Nonterminal, was not found in name map.) (Residue 78: ASN, Nonterminal, was not found in name map.) (Residue 79: ARG, Nonterminal, was not found in name map.) (Residue 80: GLU, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: LEU, Nonterminal, was not found in name map.) (Residue 83: ASP, Nonterminal, was not found in name map.) (Residue 84: GLN, Nonterminal, was not found in name map.) (Residue 85: VAL, Nonterminal, was not found in name map.) (Residue 86: GLU, Nonterminal, was not found in name map.) (Residue 87: ARG, Nonterminal, was not found in name map.) (Residue 88: GLY, Nonterminal, was not found in name map.) (Residue 89: TYR, Nonterminal, was not found in name map.) (Residue 90: ARG, Nonterminal, was not found in name map.) (Residue 91: MET, Nonterminal, was not found in name map.) (Residue 92: PRO, Nonterminal, was not found in name map.) (Residue 93: CYS, Nonterminal, was not found in name map.) (Residue 94: PRO, Nonterminal, was not found in name map.) (Residue 95: PRO, Nonterminal, was not found in name map.) (Residue 96: GLU, Nonterminal, was not found in name map.) (Residue 97: CYS, Nonterminal, was not found in name map.) (Residue 98: PRO, Nonterminal, was not found in name map.) (Residue 99: GLU, Nonterminal, was not found in name map.) (Residue 100: SER, Nonterminal, was not found in name map.) (Residue 101: LEU, Nonterminal, was not found in name map.) (Residue 102: HIS, Nonterminal, was not found in name map.) (Residue 103: ASP, Nonterminal, was not found in name map.) (Residue 104: LEU, Nonterminal, was not found in name map.) (Residue 105: MET, Nonterminal, was not found in name map.) (Residue 106: CYS, Nonterminal, was not found in name map.) (Residue 107: GLN, Nonterminal, was not found in name map.) (Residue 108: CYS, Nonterminal, was not found in name map.) (Residue 109: TRP, Nonterminal, was not found in name map.) (Residue 110: ARG, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: GLU, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: GLU, Nonterminal, was not found in name map.) (Residue 115: GLU, Nonterminal, was not found in name map.) (Residue 116: ARG, Nonterminal, was not found in name map.) (Residue 117: PRO, 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: GLU, Nonterminal, was not found in name map.) (Residue 121: TYR, Nonterminal, was not found in name map.) (Residue 122: LEU, Nonterminal, was not found in name map.) (Residue 123: GLN, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: PHE, Nonterminal, was not found in name map.) (Residue 126: LEU, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: ASP, Nonterminal, was not found in name map.) (Residue 129: TYR, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: THR, Nonterminal, was not found in name map.) (Residue 132: SER, Nonterminal, was not found in name map.) (Residue 133: THR, Nonterminal, was not found in name map.) (Residue 134: GLU, Nonterminal, was not found in name map.) (Residue 135: PRO, Nonterminal, was not found in name map.) (Residue 136: GLN, Nonterminal, was not found in name map.) (Residue 137: TYR, Nonterminal, was not found in name map.) (Residue 138: GLN, Nonterminal, was not found in name map.) (Residue 139: PRO, Nonterminal, was not found in name map.) (Residue 140: GLY, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) Mapped residue LEU, term: Terminal/last, seq. number: 143 to: CLEU. Joining NALA - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - VAL Joining VAL - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - LEU Joining LEU - VAL Joining VAL - CYS Joining CYS - LYS Joining LYS - VAL Joining VAL - ALA Joining ALA - ASP Joining ASP - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - ASN Joining ASN - GLU Joining GLU - TYR Joining TYR - THR Joining THR - ALA Joining ALA - ARG Joining ARG - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - LYS Joining LYS - PHE Joining PHE - PRO Joining PRO - ILE Joining ILE - LYS Joining LYS - TRP Joining TRP - THR Joining THR - ALA Joining ALA - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - TYR Joining TYR - GLY Joining GLY - ARG Joining ARG - PHE Joining PHE - THR Joining THR - ILE Joining ILE - LYS Joining LYS - SER Joining SER - ASP Joining ASP - VAL Joining VAL - TRP Joining TRP - SER Joining SER - PHE Joining PHE - GLY Joining GLY - ILE Joining ILE - LEU Joining LEU - LEU Joining LEU - THR Joining THR - GLU Joining GLU - LEU Joining LEU - THR Joining THR - THR Joining THR - LYS Joining LYS - GLY Joining GLY - ARG Joining ARG - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - MET Joining MET - VAL Joining VAL - ASN Joining ASN - ARG Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ARG - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - VAL Joining VAL - LEU Joining LEU - ASP Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ASP - GLN Joining GLN - VAL Joining VAL - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ARG Joining ARG - GLY Joining GLY - TYR Joining TYR - ARG Joining ARG - MET Joining MET - PRO Joining PRO - CYS Joining CYS - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - CYS Joining CYS - PRO Joining PRO - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - SER Joining SER - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - LEU Joining LEU - MET Joining MET - CYS Joining CYS - GLN Joining GLN - CYS Joining CYS - TRP Joining TRP - ARG Joining ARG - LYS Joining LYS - GLU Joining GLU - PRO Joining PRO - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - PRO Joining PRO - THR Joining THR - PHE Joining PHE - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - GLN Joining GLN - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - TYR Joining TYR - PHE Joining PHE - THR Joining THR - SER Joining SER - THR Joining THR - GLU Joining GLU - PRO Joining PRO - GLN Joining GLN - TYR Joining TYR - GLN Joining GLN - PRO Joining PRO - GLY Joining GLY - GLU Joining GLU - ASN Joining ASN - CLEU total atoms in file: 1148 Leap added 1149 missing atoms according to residue templates: 19 Heavy 1130 H / lone pairs > > logfile leapante.log