log started: Thu Feb 7 11:34:11 2013 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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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: /opt/trishamber10/amber10/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/trishamber10/amber10/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 > > set default PBradii mbondi2 Using H(N)-modified Bondi radii > pdna = loadPdb file_rev.pdb Loading PDB file: ./file_rev.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue DC, term: Terminal/beginning, seq. number: 0 to: DC5. (Residue 1: DG, Nonterminal, was not found in name map.) (Residue 2: DT, Nonterminal, was not found in name map.) (Residue 3: DG, Nonterminal, was not found in name map.) (Residue 4: DA, Nonterminal, was not found in name map.) (Residue 5: DG, Nonterminal, was not found in name map.) (Residue 6: DC, Nonterminal, was not found in name map.) (Residue 7: DA, Nonterminal, was not found in name map.) (Residue 8: DT, Nonterminal, was not found in name map.) (Residue 9: DG, Nonterminal, was not found in name map.) (Residue 10: DC, Nonterminal, was not found in name map.) (Residue 11: DT, Nonterminal, was not found in name map.) (Residue 12: DC, Nonterminal, was not found in name map.) (Residue 13: DA, Nonterminal, was not found in name map.) Mapped residue DC, term: Terminal/last, seq. number: 14 to: DC3. Mapped residue DG, term: Terminal/beginning, seq. number: 15 to: DG5. (Residue 16: DT, Nonterminal, was not found in name map.) (Residue 17: DG, Nonterminal, was not found in name map.) (Residue 18: DA, Nonterminal, was not found in name map.) (Residue 19: DG, Nonterminal, was not found in name map.) (Residue 20: DC, Nonterminal, was not found in name map.) (Residue 21: DA, Nonterminal, was not found in name map.) (Residue 22: DT, Nonterminal, was not found in name map.) (Residue 23: DG, Nonterminal, was not found in name map.) (Residue 24: DC, Nonterminal, was not found in name map.) (Residue 25: DT, Nonterminal, was not found in name map.) (Residue 26: DC, Nonterminal, was not found in name map.) Mapped residue DA, term: Terminal/last, seq. number: 27 to: DA3. Mapped residue GLN, term: Terminal/beginning, seq. number: 28 to: NGLN. (Residue 29: LYS, Nonterminal, was not found in name map.) (Residue 30: THR, Nonterminal, was not found in name map.) (Residue 31: TYR, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ASN, Nonterminal, was not found in name map.) (Residue 35: TYR, Nonterminal, was not found in name map.) (Residue 36: GLY, Nonterminal, was not found in name map.) (Residue 37: PHE, Nonterminal, was not found in name map.) (Residue 38: HIS, Nonterminal, was not found in name map.) (Residue 39: LEU, Nonterminal, was not found in name map.) (Residue 40: GLY, Nonterminal, was not found in name map.) (Residue 41: PHE, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: GLN, Nonterminal, was not found in name map.) Mapped residue SER, term: Terminal/last, seq. number: 44 to: CSER. Mapped residue VAL, term: Terminal/beginning, seq. number: 45 to: NVAL. (Residue 46: MET, Nonterminal, was not found in name map.) (Residue 47: CYS, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: TYR, Nonterminal, was not found in name map.) (Residue 50: SER, Nonterminal, was not found in name map.) (Residue 51: PRO, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: LEU, Nonterminal, was not found in name map.) (Residue 54: ASN, Nonterminal, was not found in name map.) (Residue 55: LYS, Nonterminal, was not found in name map.) (Residue 56: LEU, Nonterminal, was not found in name map.) (Residue 57: PHE, Nonterminal, was not found in name map.) (Residue 58: CYS, Nonterminal, was not found in name map.) (Residue 59: GLN, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: ALA, Nonterminal, was not found in name map.) (Residue 62: LYS, Nonterminal, was not found in name map.) (Residue 63: THR, Nonterminal, was not found in name map.) (Residue 64: CYS, Nonterminal, was not found in name map.) (Residue 65: PRO, Nonterminal, was not found in name map.) (Residue 66: VAL, Nonterminal, was not found in name map.) (Residue 67: GLN, Nonterminal, was not found in name map.) (Residue 68: LEU, Nonterminal, was not found in name map.) (Residue 69: TRP, Nonterminal, was not found in name map.) (Residue 70: VAL, Nonterminal, was not found in name map.) (Residue 71: SER, Nonterminal, was not found in name map.) (Residue 72: ALA, Nonterminal, was not found in name map.) (Residue 73: THR, Nonterminal, was not found in name map.) (Residue 74: PRO, Nonterminal, was not found in name map.) (Residue 75: PRO, Nonterminal, was not found in name map.) (Residue 76: ALA, Nonterminal, was not found in name map.) (Residue 77: GLY, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: ARG, Nonterminal, was not found in name map.) (Residue 80: VAL, Nonterminal, was not found in name map.) (Residue 81: ARG, Nonterminal, was not found in name map.) (Residue 82: ALA, Nonterminal, was not found in name map.) (Residue 83: MET, Nonterminal, was not found in name map.) (Residue 84: ALA, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: TYR, Nonterminal, was not found in name map.) (Residue 87: LYS, Nonterminal, was not found in name map.) (Residue 88: LYS, Nonterminal, was not found in name map.) (Residue 89: SER, Nonterminal, was not found in name map.) (Residue 90: GLN, Nonterminal, was not found in name map.) (Residue 91: HIS, Nonterminal, was not found in name map.) (Residue 92: MET, Nonterminal, was not found in name map.) (Residue 93: THR, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: VAL, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ARG, Nonterminal, was not found in name map.) (Residue 99: CYM, Nonterminal, was not found in name map.) (Residue 100: PRO, Nonterminal, was not found in name map.) (Residue 101: HIS, Nonterminal, was not found in name map.) (Residue 102: HIE, Nonterminal, was not found in name map.) (Residue 103: GLU, Nonterminal, was not found in name map.) (Residue 104: ARG, Nonterminal, was not found in name map.) (Residue 105: CYS, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: ASP, Nonterminal, was not found in name map.) (Residue 108: GLY, Nonterminal, was not found in name map.) (Residue 109: ASP, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: LEU, Nonterminal, was not found in name map.) (Residue 112: ALA, Nonterminal, was not found in name map.) (Residue 113: PRO, Nonterminal, was not found in name map.) (Residue 114: PRO, Nonterminal, was not found in name map.) (Residue 115: GLN, Nonterminal, was not found in name map.) (Residue 116: HIS, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: ARG, Nonterminal, was not found in name map.) (Residue 120: VAL, Nonterminal, was not found in name map.) (Residue 121: GLU, Nonterminal, was not found in name map.) (Residue 122: GLY, Nonterminal, was not found in name map.) (Residue 123: ASN, Nonterminal, was not found in name map.) (Residue 124: LEU, Nonterminal, was not found in name map.) (Residue 125: TYR, Nonterminal, was not found in name map.) (Residue 126: PRO, Nonterminal, was not found in name map.) (Residue 127: GLU, Nonterminal, was not found in name map.) (Residue 128: TYR, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: GLU, Nonterminal, was not found in name map.) (Residue 131: ASP, Nonterminal, was not found in name map.) (Residue 132: ARG, Nonterminal, was not found in name map.) (Residue 133: GLN, Nonterminal, was not found in name map.) (Residue 134: THR, Nonterminal, was not found in name map.) (Residue 135: PHE, Nonterminal, was not found in name map.) (Residue 136: ARG, Nonterminal, was not found in name map.) (Residue 137: HIS, Nonterminal, was not found in name map.) (Residue 138: SER, Nonterminal, was not found in name map.) (Residue 139: VAL, Nonterminal, was not found in name map.) (Residue 140: VAL, Nonterminal, was not found in name map.) (Residue 141: VAL, Nonterminal, was not found in name map.) (Residue 142: PRO, Nonterminal, was not found in name map.) (Residue 143: TYR, Nonterminal, was not found in name map.) (Residue 144: GLU, Nonterminal, was not found in name map.) (Residue 145: PRO, Nonterminal, was not found in name map.) (Residue 146: PRO, Nonterminal, was not found in name map.) (Residue 147: GLU, Nonterminal, was not found in name map.) (Residue 148: ALA, Nonterminal, was not found in name map.) (Residue 149: GLY, Nonterminal, was not found in name map.) (Residue 150: SER, Nonterminal, was not found in name map.) (Residue 151: GLU, Nonterminal, was not found in name map.) (Residue 152: TYR, Nonterminal, was not found in name map.) (Residue 153: THR, Nonterminal, was not found in name map.) (Residue 154: THR, Nonterminal, was not found in name map.) (Residue 155: ILE, Nonterminal, was not found in name map.) (Residue 156: HIS, Nonterminal, was not found in name map.) (Residue 157: TYR, Nonterminal, was not found in name map.) (Residue 158: LYS, Nonterminal, was not found in name map.) (Residue 159: TYR, Nonterminal, was not found in name map.) (Residue 160: MET, Nonterminal, was not found in name map.) (Residue 161: CYM, Nonterminal, was not found in name map.) (Residue 162: ASN, Nonterminal, was not found in name map.) (Residue 163: SER, Nonterminal, was not found in name map.) (Residue 164: SER, Nonterminal, was not found in name map.) (Residue 165: CYM, Nonterminal, was not found in name map.) (Residue 166: MET, Nonterminal, was not found in name map.) (Residue 167: GLY, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: MET, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: ARG, Nonterminal, was not found in name map.) (Residue 172: ARG, Nonterminal, was not found in name map.) (Residue 173: PRO, Nonterminal, was not found in name map.) (Residue 174: ILE, Nonterminal, was not found in name map.) (Residue 175: LEU, Nonterminal, was not found in name map.) (Residue 176: THR, Nonterminal, was not found in name map.) (Residue 177: ILE, Nonterminal, was not found in name map.) (Residue 178: ILE, Nonterminal, was not found in name map.) (Residue 179: THR, Nonterminal, was not found in name map.) (Residue 180: LEU, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: ASP, Nonterminal, was not found in name map.) (Residue 183: SER, Nonterminal, was not found in name map.) (Residue 184: SER, Nonterminal, was not found in name map.) (Residue 185: GLY, Nonterminal, was not found in name map.) (Residue 186: ASN, Nonterminal, was not found in name map.) (Residue 187: LEU, Nonterminal, was not found in name map.) (Residue 188: LEU, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: ARG, Nonterminal, was not found in name map.) (Residue 191: ASP, Nonterminal, was not found in name map.) (Residue 192: SER, Nonterminal, was not found in name map.) (Residue 193: PHE, Nonterminal, was not found in name map.) (Residue 194: GLU, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: ARG, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: CYS, Nonterminal, was not found in name map.) (Residue 199: ALA, Nonterminal, was not found in name map.) (Residue 200: CYS, Nonterminal, was not found in name map.) (Residue 201: PRO, Nonterminal, was not found in name map.) (Residue 202: GLY, Nonterminal, was not found in name map.) (Residue 203: ARG, Nonterminal, was not found in name map.) (Residue 204: ASP, Nonterminal, was not found in name map.) (Residue 205: ARG, Nonterminal, was not found in name map.) (Residue 206: ARG, Nonterminal, was not found in name map.) (Residue 207: THR, Nonterminal, was not found in name map.) (Residue 208: GLU, Nonterminal, was not found in name map.) (Residue 209: GLU, Nonterminal, was not found in name map.) (Residue 210: GLU, Nonterminal, was not found in name map.) (Residue 211: ASN, Nonterminal, was not found in name map.) (Residue 212: PHE, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: LYS, Nonterminal, was not found in name map.) Mapped residue LYS, term: Terminal/last, seq. number: 215 to: CLYS. Mapped residue GLN, term: Terminal/beginning, seq. number: 216 to: NGLN. (Residue 217: LYS, Nonterminal, was not found in name map.) (Residue 218: THR, Nonterminal, was not found in name map.) (Residue 219: TYR, Nonterminal, was not found in name map.) (Residue 220: GLN, Nonterminal, was not found in name map.) (Residue 221: GLY, Nonterminal, was not found in name map.) (Residue 222: ASN, Nonterminal, was not found in name map.) (Residue 223: TYR, Nonterminal, was not found in name map.) (Residue 224: GLY, Nonterminal, was not found in name map.) (Residue 225: PHE, Nonterminal, was not found in name map.) (Residue 226: HIS, Nonterminal, was not found in name map.) (Residue 227: LEU, Nonterminal, was not found in name map.) (Residue 228: GLY, Nonterminal, was not found in name map.) (Residue 229: PHE, Nonterminal, was not found in name map.) (Residue 230: LEU, Nonterminal, was not found in name map.) (Residue 231: GLN, Nonterminal, was not found in name map.) Mapped residue SER, term: Terminal/last, seq. number: 232 to: CSER. Mapped residue VAL, term: Terminal/beginning, seq. number: 233 to: NVAL. (Residue 234: MET, Nonterminal, was not found in name map.) (Residue 235: CYS, Nonterminal, was not found in name map.) (Residue 236: THR, Nonterminal, was not found in name map.) (Residue 237: TYR, Nonterminal, was not found in name map.) (Residue 238: SER, Nonterminal, was not found in name map.) (Residue 239: PRO, Nonterminal, was not found in name map.) (Residue 240: PRO, Nonterminal, was not found in name map.) (Residue 241: LEU, Nonterminal, was not found in name map.) (Residue 242: ASN, Nonterminal, was not found in name map.) (Residue 243: LYS, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: PHE, Nonterminal, was not found in name map.) (Residue 246: CYS, Nonterminal, was not found in name map.) (Residue 247: GLN, Nonterminal, was not found in name map.) (Residue 248: LEU, Nonterminal, was not found in name map.) (Residue 249: ALA, Nonterminal, was not found in name map.) (Residue 250: LYS, Nonterminal, was not found in name map.) (Residue 251: THR, Nonterminal, was not found in name map.) (Residue 252: CYS, Nonterminal, was not found in name map.) (Residue 253: PRO, Nonterminal, was not found in name map.) (Residue 254: VAL, Nonterminal, was not found in name map.) (Residue 255: GLN, Nonterminal, was not found in name map.) (Residue 256: LEU, Nonterminal, was not found in name map.) (Residue 257: TRP, Nonterminal, was not found in name map.) (Residue 258: VAL, Nonterminal, was not found in name map.) (Residue 259: SER, Nonterminal, was not found in name map.) (Residue 260: ALA, Nonterminal, was not found in name map.) (Residue 261: THR, Nonterminal, was not found in name map.) (Residue 262: PRO, Nonterminal, was not found in name map.) (Residue 263: PRO, Nonterminal, was not found in name map.) (Residue 264: ALA, Nonterminal, was not found in name map.) (Residue 265: GLY, Nonterminal, was not found in name map.) (Residue 266: SER, Nonterminal, was not found in name map.) (Residue 267: ARG, Nonterminal, was not found in name map.) (Residue 268: VAL, Nonterminal, was not found in name map.) (Residue 269: ARG, Nonterminal, was not found in name map.) (Residue 270: ALA, Nonterminal, was not found in name map.) (Residue 271: MET, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: ILE, Nonterminal, was not found in name map.) (Residue 274: TYR, Nonterminal, was not found in name map.) (Residue 275: LYS, Nonterminal, was not found in name map.) (Residue 276: LYS, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: GLN, Nonterminal, was not found in name map.) (Residue 279: HIS, Nonterminal, was not found in name map.) (Residue 280: MET, Nonterminal, was not found in name map.) (Residue 281: THR, Nonterminal, was not found in name map.) (Residue 282: GLU, Nonterminal, was not found in name map.) (Residue 283: VAL, Nonterminal, was not found in name map.) (Residue 284: VAL, Nonterminal, was not found in name map.) (Residue 285: ARG, Nonterminal, was not found in name map.) (Residue 286: ARG, Nonterminal, was not found in name map.) (Residue 287: CYM, Nonterminal, was not found in name map.) (Residue 288: PRO, Nonterminal, was not found in name map.) (Residue 289: HIS, Nonterminal, was not found in name map.) (Residue 290: HIE, Nonterminal, was not found in name map.) (Residue 291: GLU, Nonterminal, was not found in name map.) (Residue 292: ARG, Nonterminal, was not found in name map.) (Residue 293: CYS, Nonterminal, was not found in name map.) (Residue 294: SER, Nonterminal, was not found in name map.) (Residue 295: ASP, Nonterminal, was not found in name map.) (Residue 296: GLY, Nonterminal, was not found in name map.) (Residue 297: ASP, Nonterminal, was not found in name map.) (Residue 298: GLY, Nonterminal, was not found in name map.) (Residue 299: LEU, Nonterminal, was not found in name map.) (Residue 300: ALA, Nonterminal, was not found in name map.) (Residue 301: PRO, Nonterminal, was not found in name map.) (Residue 302: PRO, Nonterminal, was not found in name map.) (Residue 303: GLN, Nonterminal, was not found in name map.) (Residue 304: HIS, Nonterminal, was not found in name map.) (Residue 305: LEU, Nonterminal, was not found in name map.) (Residue 306: ILE, Nonterminal, was not found in name map.) (Residue 307: ARG, Nonterminal, was not found in name map.) (Residue 308: VAL, Nonterminal, was not found in name map.) (Residue 309: GLU, Nonterminal, was not found in name map.) (Residue 310: GLY, Nonterminal, was not found in name map.) (Residue 311: ASN, Nonterminal, was not found in name map.) (Residue 312: LEU, Nonterminal, was not found in name map.) (Residue 313: TYR, Nonterminal, was not found in name map.) (Residue 314: PRO, Nonterminal, was not found in name map.) (Residue 315: GLU, Nonterminal, was not found in name map.) (Residue 316: TYR, Nonterminal, was not found in name map.) (Residue 317: LEU, Nonterminal, was not found in name map.) (Residue 318: GLU, Nonterminal, was not found in name map.) (Residue 319: ASP, Nonterminal, was not found in name map.) (Residue 320: ARG, Nonterminal, was not found in name map.) (Residue 321: GLN, Nonterminal, was not found in name map.) (Residue 322: THR, Nonterminal, was not found in name map.) (Residue 323: PHE, Nonterminal, was not found in name map.) (Residue 324: ARG, Nonterminal, was not found in name map.) (Residue 325: HIS, Nonterminal, was not found in name map.) (Residue 326: SER, Nonterminal, was not found in name map.) (Residue 327: VAL, Nonterminal, was not found in name map.) (Residue 328: VAL, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: PRO, Nonterminal, was not found in name map.) (Residue 331: TYR, Nonterminal, was not found in name map.) (Residue 332: GLU, Nonterminal, was not found in name map.) (Residue 333: PRO, Nonterminal, was not found in name map.) (Residue 334: PRO, Nonterminal, was not found in name map.) (Residue 335: GLU, Nonterminal, was not found in name map.) (Residue 336: ALA, Nonterminal, was not found in name map.) (Residue 337: GLY, Nonterminal, was not found in name map.) (Residue 338: SER, Nonterminal, was not found in name map.) (Residue 339: GLU, Nonterminal, was not found in name map.) (Residue 340: TYR, Nonterminal, was not found in name map.) (Residue 341: THR, Nonterminal, was not found in name map.) (Residue 342: THR, Nonterminal, was not found in name map.) (Residue 343: ILE, Nonterminal, was not found in name map.) (Residue 344: HIS, Nonterminal, was not found in name map.) (Residue 345: TYR, Nonterminal, was not found in name map.) (Residue 346: LYS, Nonterminal, was not found in name map.) (Residue 347: TYR, Nonterminal, was not found in name map.) (Residue 348: MET, Nonterminal, was not found in name map.) (Residue 349: CYM, Nonterminal, was not found in name map.) (Residue 350: ASN, Nonterminal, was not found in name map.) (Residue 351: SER, Nonterminal, was not found in name map.) (Residue 352: SER, Nonterminal, was not found in name map.) (Residue 353: CYM, Nonterminal, was not found in name map.) (Residue 354: MET, Nonterminal, was not found in name map.) (Residue 355: GLY, Nonterminal, was not found in name map.) (Residue 356: GLY, Nonterminal, was not found in name map.) (Residue 357: MET, Nonterminal, was not found in name map.) (Residue 358: ASN, Nonterminal, was not found in name map.) (Residue 359: ARG, Nonterminal, was not found in name map.) (Residue 360: ARG, Nonterminal, was not found in name map.) (Residue 361: PRO, Nonterminal, was not found in name map.) (Residue 362: ILE, Nonterminal, was not found in name map.) (Residue 363: LEU, Nonterminal, was not found in name map.) (Residue 364: THR, Nonterminal, was not found in name map.) (Residue 365: ILE, Nonterminal, was not found in name map.) (Residue 366: ILE, Nonterminal, was not found in name map.) (Residue 367: THR, Nonterminal, was not found in name map.) (Residue 368: LEU, Nonterminal, was not found in name map.) (Residue 369: GLU, Nonterminal, was not found in name map.) (Residue 370: ASP, Nonterminal, was not found in name map.) (Residue 371: SER, Nonterminal, was not found in name map.) (Residue 372: SER, Nonterminal, was not found in name map.) (Residue 373: GLY, Nonterminal, was not found in name map.) (Residue 374: ASN, Nonterminal, was not found in name map.) (Residue 375: LEU, Nonterminal, was not found in name map.) (Residue 376: LEU, Nonterminal, was not found in name map.) (Residue 377: GLY, Nonterminal, was not found in name map.) (Residue 378: ARG, Nonterminal, was not found in name map.) (Residue 379: ASP, Nonterminal, was not found in name map.) (Residue 380: SER, Nonterminal, was not found in name map.) (Residue 381: PHE, Nonterminal, was not found in name map.) (Residue 382: GLU, Nonterminal, was not found in name map.) (Residue 383: VAL, Nonterminal, was not found in name map.) (Residue 384: ARG, Nonterminal, was not found in name map.) (Residue 385: VAL, Nonterminal, was not found in name map.) (Residue 386: CYS, Nonterminal, was not found in name map.) (Residue 387: ALA, Nonterminal, was not found in name map.) (Residue 388: CYS, Nonterminal, was not found in name map.) (Residue 389: PRO, Nonterminal, was not found in name map.) (Residue 390: GLY, Nonterminal, was not found in name map.) (Residue 391: ARG, Nonterminal, was not found in name map.) (Residue 392: ASP, Nonterminal, was not found in name map.) (Residue 393: ARG, Nonterminal, was not found in name map.) (Residue 394: ARG, Nonterminal, was not found in name map.) (Residue 395: THR, Nonterminal, was not found in name map.) (Residue 396: GLU, Nonterminal, was not found in name map.) (Residue 397: GLU, Nonterminal, was not found in name map.) (Residue 398: GLU, Nonterminal, was not found in name map.) (Residue 399: ASN, Nonterminal, was not found in name map.) (Residue 400: PHE, Nonterminal, was not found in name map.) (Residue 401: ARG, Nonterminal, was not found in name map.) (Residue 402: LYS, Nonterminal, was not found in name map.) (Residue 403: LYS, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 404 to: CGLU. (Residue 405: ZNA, Terminal/last, was not found in name map.) Unknown residue: ZNA number: 405 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 406: ZNB, Terminal/last, was not found in name map.) Unknown residue: ZNB number: 406 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Created a new atom named: P within residue: .R Created a new atom named: OP1 within residue: .R Created a new atom named: OP2 within residue: .R Joining DC5 - DG Joining DG - DT Joining DT - DG Joining DG - DA Joining DA - DG Joining DG - DC Joining DC - DA Joining DA - DT Joining DT - DG Joining DG - DC Joining DC - DT Joining DT - DC Joining DC - DA Joining DA - DC3 Created a new atom named: P within residue: .R Created a new atom named: OP1 within residue: .R Created a new atom named: OP2 within residue: .R Joining DG5 - DT Joining DT - DG Joining DG - DA Joining DA - DG Joining DG - DC Joining DC - DA Joining DA - DT Joining DT - DG Joining DG - DC Joining DC - DT Joining DT - DC Joining DC - DA3 Joining NGLN - LYS Joining LYS - THR Joining THR - TYR Joining TYR - GLN Joining GLN - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - PHE Joining PHE - HIE Joining HIE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - CSER Added missing heavy atom: .R.A Joining NVAL - MET Joining MET - CYS Joining CYS - THR Joining THR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - PRO Joining PRO - LEU Joining LEU - ASN Joining ASN - LYS Joining LYS - LEU Joining LEU - PHE Joining PHE - CYS Joining CYS - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - LYS Joining LYS - THR Joining THR - CYS Joining CYS - PRO Joining PRO - VAL Joining VAL - GLN Joining GLN - LEU Joining LEU - TRP Joining TRP - VAL Joining VAL - SER Joining SER - ALA Joining ALA - THR Joining THR - PRO Joining PRO - PRO Joining PRO - ALA Joining ALA - GLY Joining GLY - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ARG Joining ARG - ALA Joining ALA - MET Joining MET - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - LYS Joining LYS - LYS 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 LYS - SER Joining SER - GLN Joining GLN - HIE Joining HIE - MET Joining MET - THR Joining THR - GLU Joining GLU - VAL Joining VAL - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - CYM Joining CYM - PRO Joining PRO - HIE Joining HIE - HIE Joining HIE - GLU Joining GLU - ARG Joining ARG - CYS Joining CYS - SER Joining SER - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - GLN Joining GLN - HIE Joining HIE - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - TYR Joining TYR - PRO Joining PRO - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - ARG Joining ARG - GLN Joining GLN - THR Joining THR - PHE Joining PHE - ARG Joining ARG - HIE Joining HIE - SER Joining SER - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - GLY Joining GLY - SER Joining SER - GLU Joining GLU - TYR Joining TYR - THR Joining THR - THR Joining THR - ILE Joining ILE - HIE Joining HIE - TYR Joining TYR - LYS Joining LYS - TYR Joining TYR - MET Joining MET - CYM Joining CYM - ASN Joining ASN - SER Joining SER - SER Joining SER - CYM Joining CYM - MET Joining MET - GLY Joining GLY - GLY Joining GLY - MET Joining MET - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - THR Joining THR - ILE Joining ILE - ILE Joining ILE - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - SER Joining SER - SER Joining SER - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - GLY Joining GLY - ARG Joining ARG - ASP Joining ASP - SER Joining SER - PHE Joining PHE - GLU Joining GLU - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - ALA Joining ALA - CYS Joining CYS - PRO Joining PRO - GLY Joining GLY - ARG Joining ARG - ASP Joining ASP - ARG Joining ARG - ARG Joining ARG - THR Joining THR - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - ASN Joining ASN - PHE Joining PHE - ARG Joining ARG - LYS Joining LYS - CLYS Added missing heavy atom: .R.A Joining NGLN - LYS Joining LYS - THR Joining THR - TYR Joining TYR - GLN Joining GLN - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - PHE Joining PHE - HIE Joining HIE - LEU Joining LEU - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - CSER Added missing heavy atom: .R.A Joining NVAL - MET Joining MET - CYS Joining CYS - THR Joining THR - TYR Joining TYR - SER Joining SER - PRO Joining PRO - PRO Joining PRO - LEU Joining LEU - ASN Joining ASN - LYS Joining LYS - LEU Joining LEU - PHE Joining PHE - CYS Joining CYS - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - LYS Joining LYS - THR Joining THR - CYS Joining CYS - PRO Joining PRO - VAL Joining VAL - GLN Joining GLN - LEU Joining LEU - TRP Joining TRP - VAL Joining VAL - SER Joining SER - ALA Joining ALA - THR Joining THR - PRO Joining PRO - PRO Joining PRO - ALA Joining ALA - GLY Joining GLY - SER Joining SER - ARG Joining ARG - VAL Joining VAL - ARG Joining ARG - ALA Joining ALA - MET Joining MET - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - LYS Joining LYS - LYS 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 LYS - SER Joining SER - GLN Joining GLN - HIE Joining HIE - MET Joining MET - THR Joining THR - GLU Joining GLU - VAL Joining VAL - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - CYM Joining CYM - PRO Joining PRO - HIE Joining HIE - HIE Joining HIE - GLU Joining GLU - ARG Joining ARG - CYS Joining CYS - SER Joining SER - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - LEU Joining LEU - ALA Joining ALA - PRO Joining PRO - PRO Joining PRO - GLN Joining GLN - HIE Joining HIE - LEU Joining LEU - ILE Joining ILE - ARG Joining ARG - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - TYR Joining TYR - PRO Joining PRO - GLU Joining GLU - TYR Joining TYR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - ARG Joining ARG - GLN Joining GLN - THR Joining THR - PHE Joining PHE - ARG Joining ARG - HIE Joining HIE - SER Joining SER - VAL Joining VAL - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - TYR Joining TYR - GLU Joining GLU - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - GLY Joining GLY - SER Joining SER - GLU Joining GLU - TYR Joining TYR - THR Joining THR - THR Joining THR - ILE Joining ILE - HIE Joining HIE - TYR Joining TYR - LYS Joining LYS - TYR Joining TYR - MET Joining MET - CYM Joining CYM - ASN Joining ASN - SER Joining SER - SER Joining SER - CYM Joining CYM - MET Joining MET - GLY Joining GLY - GLY Joining GLY - MET Joining MET - ASN Joining ASN - ARG Joining ARG - ARG Joining ARG - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - THR Joining THR - ILE Joining ILE - ILE Joining ILE - THR Joining THR - LEU Joining LEU - GLU Joining GLU - ASP Joining ASP - SER Joining SER - SER Joining SER - GLY Joining GLY - ASN Joining ASN - LEU Joining LEU - LEU Joining LEU - GLY Joining GLY - ARG Joining ARG - ASP Joining ASP - SER Joining SER - PHE Joining PHE - GLU Joining GLU - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - CYS Joining CYS - ALA Joining ALA - CYS Joining CYS - PRO Joining PRO - GLY Joining GLY - ARG Joining ARG - ASP Joining ASP - ARG Joining ARG - ARG Joining ARG - THR Joining THR - GLU Joining GLU - GLU Joining GLU - GLU Joining GLU - ASN Joining ASN - PHE Joining PHE - ARG Joining ARG - LYS Joining LYS - LYS Joining LYS - CGLU Added missing heavy atom: .R.A Creating new UNIT for residue: ZNA sequence: 407 Created a new atom named: ZN within residue: .R Creating new UNIT for residue: ZNB sequence: 408 Created a new atom named: ZN within residue: .R total atoms in file: 3581 Leap added 3276 missing atoms according to residue templates: 12 Heavy 3264 H / lone pairs The file contained 8 atoms not in residue templates > set pdna.ZNA.ZN type Zn > set pdna.ZNA.ZN charge 2.0000 > set pdna.ZNB.ZN type Zn > set pdna.ZNB.ZN charge 2.0000 > saveAmberParm pdna pdna.parm7 pdna.crd Checking Unit. WARNING: The unperturbed charge of the unit: -19.000000 is not zero. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A

does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. > quit Quit