log started: Sat May 11 15:46:36 2019 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # 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" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "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" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "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" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/srania/Amber/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/srania/Amber/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/amino12.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: HYP 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 aminoct12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/aminoct12.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: CHYP 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 aminont12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/aminont12.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 >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > set default PBRadii mbondi3 Using ArgH and AspGluO modified Bondi2 radii > loadAmberPrep cro.prepin Loading Prep file: ./cro.prepin Loaded UNIT: CRO > loadAmberParams frcmod2.cro Loading parameters: ./frcmod2.cro Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadAmberParams frcmod1.cro Loading parameters: ./frcmod1.cro Reading force field modification type file (frcmod) Reading title: Remark line goes here > x = loadPDB gfp.pdb Loading PDB file: ./gfp.pdb Enter zPdbReadScan from call depth 0. (starting new molecule for chain ) (starting new molecule for chain A) (starting new molecule for chain ) (starting new molecule for chain A) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER. (Residue 1: LYS, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: GLU, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: LEU, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: VAL, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: ILE, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: VAL, Nonterminal, was not found in name map.) (Residue 15: GLU, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: GLY, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: GLY, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: PHE, Nonterminal, was not found in name map.) (Residue 26: SER, Nonterminal, was not found in name map.) (Residue 27: VAL, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: GLY, Nonterminal, was not found in name map.) (Residue 30: GLU, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ASP, Nonterminal, was not found in name map.) (Residue 35: ALA, Nonterminal, was not found in name map.) (Residue 36: THR, Nonterminal, was not found in name map.) (Residue 37: TYR, Nonterminal, was not found in name map.) (Residue 38: GLY, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: LEU, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: PHE, Nonterminal, was not found in name map.) (Residue 45: ILE, Nonterminal, was not found in name map.) (Residue 46: CYS, Nonterminal, was not found in name map.) (Residue 47: THR, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LYS, Nonterminal, was not found in name map.) (Residue 51: LEU, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: PRO, Nonterminal, was not found in name map.) (Residue 55: TRP, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: VAL, Nonterminal, was not found in name map.) (Residue 60: THR, Nonterminal, was not found in name map.) (Residue 61: THR, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: CRO, Terminal/last, was not found in name map.) Mapped residue VAL, term: Terminal/beginning, seq. number: 64 to: NVAL. (Residue 65: GLN, Nonterminal, was not found in name map.) (Residue 66: CYS, Nonterminal, was not found in name map.) (Residue 67: PHE, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: ARG, 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: ASP, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 74 to: CMET. Mapped residue LYS, term: Terminal/beginning, seq. number: 75 to: NLYS. (Residue 76: ARG, Nonterminal, was not found in name map.) (Residue 77: HIE, Nonterminal, was not found in name map.) (Residue 78: ASP, Nonterminal, was not found in name map.) (Residue 79: PHE, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: LYS, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: ALA, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 84 to: CMET. (Residue 85: ME, Terminal/last, was not found in name map.) Unknown residue: ME number: 85 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Mapped residue MET, term: Terminal/last, seq. number: 86 to: CMET. Mapped residue PRO, term: Terminal/beginning, seq. number: 87 to: NPRO. (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: GLY, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: VAL, Nonterminal, was not found in name map.) (Residue 92: GLN, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: THR, Nonterminal, was not found in name map.) (Residue 96: ILE, Nonterminal, was not found in name map.) (Residue 97: PHE, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ASP, Nonterminal, was not found in name map.) (Residue 101: ASP, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: ASN, Nonterminal, was not found in name map.) (Residue 104: TYR, Nonterminal, was not found in name map.) (Residue 105: LYS, Nonterminal, was not found in name map.) (Residue 106: THR, Nonterminal, was not found in name map.) (Residue 107: ARG, Nonterminal, was not found in name map.) (Residue 108: ALA, Nonterminal, was not found in name map.) (Residue 109: GLU, Nonterminal, was not found in name map.) (Residue 110: VAL, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: PHE, Nonterminal, was not found in name map.) (Residue 113: GLU, Nonterminal, was not found in name map.) (Residue 114: GLY, Nonterminal, was not found in name map.) (Residue 115: ASP, Nonterminal, was not found in name map.) (Residue 116: THR, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: ASN, Nonterminal, was not found in name map.) (Residue 120: ARG, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: LEU, Nonterminal, was not found in name map.) (Residue 124: LYS, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ILE, Nonterminal, was not found in name map.) (Residue 127: ASP, Nonterminal, was not found in name map.) (Residue 128: PHE, Nonterminal, was not found in name map.) (Residue 129: LYS, 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: GLY, Nonterminal, was not found in name map.) (Residue 133: ASN, Nonterminal, was not found in name map.) (Residue 134: ILE, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: GLY, Nonterminal, was not found in name map.) (Residue 137: HID, Nonterminal, was not found in name map.) (Residue 138: LYS, Nonterminal, was not found in name map.) (Residue 139: LEU, Nonterminal, was not found in name map.) (Residue 140: GLU, Nonterminal, was not found in name map.) (Residue 141: TYR, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) (Residue 143: TYR, Nonterminal, was not found in name map.) (Residue 144: ASN, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: HID, Nonterminal, was not found in name map.) (Residue 147: ASN, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: TYR, Nonterminal, was not found in name map.) (Residue 150: ILE, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 151 to: CMET. Mapped residue ALA, term: Terminal/beginning, seq. number: 152 to: NALA. (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: LYS, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: LYS, Nonterminal, was not found in name map.) (Residue 157: ASN, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ILE, Nonterminal, was not found in name map.) (Residue 160: LYS, Nonterminal, was not found in name map.) (Residue 161: VAL, Nonterminal, was not found in name map.) (Residue 162: ASN, Nonterminal, was not found in name map.) (Residue 163: PHE, Nonterminal, was not found in name map.) (Residue 164: LYS, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ARG, Nonterminal, was not found in name map.) (Residue 167: HIE, Nonterminal, was not found in name map.) (Residue 168: ASN, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: GLU, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: GLY, Nonterminal, was not found in name map.) (Residue 173: SER, Nonterminal, was not found in name map.) (Residue 174: VAL, Nonterminal, was not found in name map.) (Residue 175: GLN, Nonterminal, was not found in name map.) (Residue 176: LEU, Nonterminal, was not found in name map.) (Residue 177: ALA, Nonterminal, was not found in name map.) (Residue 178: ASP, Nonterminal, was not found in name map.) (Residue 179: HID, Nonterminal, was not found in name map.) (Residue 180: TYR, Nonterminal, was not found in name map.) (Residue 181: GLN, Nonterminal, was not found in name map.) (Residue 182: GLN, Nonterminal, was not found in name map.) (Residue 183: ASN, Nonterminal, was not found in name map.) (Residue 184: THR, Nonterminal, was not found in name map.) (Residue 185: PRO, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: GLY, Nonterminal, was not found in name map.) (Residue 188: ASP, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: LEU, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: ASP, Nonterminal, was not found in name map.) (Residue 196: ASN, Nonterminal, was not found in name map.) (Residue 197: HID, Nonterminal, was not found in name map.) (Residue 198: TYR, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: SER, Nonterminal, was not found in name map.) (Residue 201: THR, Nonterminal, was not found in name map.) (Residue 202: GLN, Nonterminal, was not found in name map.) (Residue 203: SER, Nonterminal, was not found in name map.) (Residue 204: ALA, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: SER, Nonterminal, was not found in name map.) (Residue 207: LYS, Nonterminal, was not found in name map.) (Residue 208: ASP, 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: GLU, Nonterminal, was not found in name map.) (Residue 212: LYS, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: ASP, Nonterminal, was not found in name map.) (Residue 215: HID, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 216 to: CMET. (Residue 217: ME, Terminal/last, was not found in name map.) Unknown residue: ME number: 217 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Mapped residue MET, term: Terminal/last, seq. number: 218 to: CMET. Mapped residue VAL, term: Terminal/beginning, seq. number: 219 to: NVAL. (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: GLU, Nonterminal, was not found in name map.) (Residue 223: PHE, Nonterminal, was not found in name map.) (Residue 224: VAL, Nonterminal, was not found in name map.) (Residue 225: THR, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: ALA, Nonterminal, was not found in name map.) (Residue 228: GLY, Nonterminal, was not found in name map.) Mapped residue ILE, term: Terminal/last, seq. number: 229 to: CILE. Joining NSER - LYS Joining LYS - GLY Joining GLY - GLU Joining GLU - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - LEU Joining LEU - PHE Joining PHE - THR Joining THR - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - ASN Joining ASN - GLY Joining GLY - HIE Joining HIE - LYS Added missing heavy atom: .R.A Joining LYS - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - ASP Joining ASP - ALA Joining ALA - THR Joining THR - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - THR Joining THR - LEU Joining LEU - LYS Joining LYS - PHE Joining PHE - ILE Joining ILE - CYS Joining CYS - THR Joining THR - THR Joining THR - GLY Joining GLY - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - TRP Joining TRP - PRO Joining PRO - THR Joining THR - LEU Joining LEU - VAL Joining VAL - THR Joining THR - THR Joining THR - PHE Joining PHE - CRO Joining NVAL - GLN Joining GLN - CYS Joining CYS - PHE Joining PHE - SER Joining SER - ARG Joining ARG - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - HIE Joining HIE - CMET Created a new atom named: SE within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NLYS - ARG Joining ARG - HIE Joining HIE - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - LYS Joining LYS - SER Joining SER - ALA Joining ALA - CMET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: ME sequence: 86 Created a new atom named: SD within residue: .R 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NPRO - GLU Joining GLU - GLY Joining GLY - TYR Joining TYR - VAL Joining VAL - GLN Joining GLN - GLU Joining GLU - ARG Joining ARG - THR Joining THR - ILE Joining ILE - PHE Joining PHE - PHE Joining PHE - LYS Added missing heavy atom: .R.A Joining LYS - ASP Joining ASP - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - THR Joining THR - ARG Joining ARG - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - PHE Joining PHE - GLU Joining GLU - GLY Joining GLY - ASP Joining ASP - THR Joining THR - LEU Joining LEU - 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 Joining ARG - ILE Joining ILE - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - LEU Joining LEU - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - PHE Joining PHE - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - HID Joining HID - LYS Joining LYS - LEU Joining LEU - GLU Joining GLU - TYR Joining TYR - ASN Joining ASN - TYR Joining TYR - ASN Joining ASN - SER Joining SER - HID Joining HID - ASN Joining ASN - VAL Joining VAL - TYR Joining TYR - ILE Joining ILE - CMET Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NALA - ASP Joining ASP - 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 - GLN 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 GLN - 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 Added missing heavy atom: .R.A Joining LYS - ASN Joining ASN - GLY Joining GLY - ILE Joining ILE - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - VAL Joining VAL - ASN Joining ASN - PHE Joining PHE - LYS Joining LYS - ILE Joining ILE - ARG Joining ARG - HIE Joining HIE - ASN Joining ASN - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - GLY Joining GLY - SER Joining SER - VAL Joining VAL - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - HID Joining HID - TYR Joining TYR - GLN Joining GLN - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - ILE Joining ILE - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - ASP Joining ASP - ASN Joining ASN - HID Joining HID - TYR Joining TYR - LEU Joining LEU - SER Joining SER - THR Joining THR - GLN Joining GLN - SER Joining SER - ALA Joining ALA - LEU Joining LEU - SER Joining SER - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - ASN Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ASN - GLU Joining GLU - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - ARG Joining ARG - ASP Joining ASP - HID Joining HID - CMET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: ME sequence: 218 Created a new atom named: SD within residue: .R 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NVAL - LEU Joining LEU - LEU Joining LEU - GLU Joining GLU - PHE Joining PHE - VAL Joining VAL - THR Joining THR - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - CILE Added missing heavy atom: .R.A total atoms in file: 3440 Leap added 195 missing atoms according to residue templates: 69 Heavy 126 H / lone pairs The file contained 6 atoms not in residue templates > saveAmberParm x gfp.parm7 gfp.rst7 Checking Unit. WARNING: There is a bond of 4.982997 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.615864 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.428284 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 6.282434 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.254820 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.171454 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.659759 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.853690 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -7.000003 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 log started: Sat May 11 15:48:27 2019 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # 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" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "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" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "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" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/srania/Amber/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/srania/Amber/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/amino12.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: HYP 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 aminoct12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/aminoct12.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: CHYP 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 aminont12.lib Loading library: /home/srania/Amber/amber16/dat/leap/lib/aminont12.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 >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > set default PBRadii mbondi3 Using ArgH and AspGluO modified Bondi2 radii > loadAmberPrep cro.prepin Loading Prep file: ./cro.prepin Loaded UNIT: CRO > loadAmberParams frcmod2.cro Loading parameters: ./frcmod2.cro Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadAmberParams frcmod1.cro Loading parameters: ./frcmod1.cro Reading force field modification type file (frcmod) Reading title: Remark line goes here > x = loadPDB gfp.pdb Loading PDB file: ./gfp.pdb Enter zPdbReadScan from call depth 0. (starting new molecule for chain ) (starting new molecule for chain A) (starting new molecule for chain ) (starting new molecule for chain A) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER. (Residue 1: LYS, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: GLU, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: LEU, Nonterminal, was not found in name map.) (Residue 6: PHE, Nonterminal, was not found in name map.) (Residue 7: THR, Nonterminal, was not found in name map.) (Residue 8: GLY, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: VAL, Nonterminal, was not found in name map.) (Residue 11: PRO, Nonterminal, was not found in name map.) (Residue 12: ILE, Nonterminal, was not found in name map.) (Residue 13: LEU, Nonterminal, was not found in name map.) (Residue 14: VAL, Nonterminal, was not found in name map.) (Residue 15: GLU, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: ASP, Nonterminal, was not found in name map.) (Residue 18: GLY, Nonterminal, was not found in name map.) (Residue 19: ASP, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: ASN, Nonterminal, was not found in name map.) (Residue 22: GLY, Nonterminal, was not found in name map.) (Residue 23: HIE, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: PHE, Nonterminal, was not found in name map.) (Residue 26: SER, Nonterminal, was not found in name map.) (Residue 27: VAL, Nonterminal, was not found in name map.) (Residue 28: SER, Nonterminal, was not found in name map.) (Residue 29: GLY, Nonterminal, was not found in name map.) (Residue 30: GLU, Nonterminal, was not found in name map.) (Residue 31: GLY, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ASP, Nonterminal, was not found in name map.) (Residue 35: ALA, Nonterminal, was not found in name map.) (Residue 36: THR, Nonterminal, was not found in name map.) (Residue 37: TYR, Nonterminal, was not found in name map.) (Residue 38: GLY, Nonterminal, was not found in name map.) (Residue 39: LYS, Nonterminal, was not found in name map.) (Residue 40: LEU, Nonterminal, was not found in name map.) (Residue 41: THR, Nonterminal, was not found in name map.) (Residue 42: LEU, Nonterminal, was not found in name map.) (Residue 43: LYS, Nonterminal, was not found in name map.) (Residue 44: PHE, Nonterminal, was not found in name map.) (Residue 45: ILE, Nonterminal, was not found in name map.) (Residue 46: CYS, Nonterminal, was not found in name map.) (Residue 47: THR, Nonterminal, was not found in name map.) (Residue 48: THR, Nonterminal, was not found in name map.) (Residue 49: GLY, Nonterminal, was not found in name map.) (Residue 50: LYS, Nonterminal, was not found in name map.) (Residue 51: LEU, Nonterminal, was not found in name map.) (Residue 52: PRO, Nonterminal, was not found in name map.) (Residue 53: VAL, Nonterminal, was not found in name map.) (Residue 54: PRO, Nonterminal, was not found in name map.) (Residue 55: TRP, Nonterminal, was not found in name map.) (Residue 56: PRO, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: VAL, Nonterminal, was not found in name map.) (Residue 60: THR, Nonterminal, was not found in name map.) (Residue 61: THR, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: CRO, Terminal/last, was not found in name map.) Mapped residue VAL, term: Terminal/beginning, seq. number: 64 to: NVAL. (Residue 65: GLN, Nonterminal, was not found in name map.) (Residue 66: CYS, Nonterminal, was not found in name map.) (Residue 67: PHE, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: ARG, 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: ASP, Nonterminal, was not found in name map.) (Residue 73: HIE, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 74 to: CMET. Mapped residue LYS, term: Terminal/beginning, seq. number: 75 to: NLYS. (Residue 76: ARG, Nonterminal, was not found in name map.) (Residue 77: HIE, Nonterminal, was not found in name map.) (Residue 78: ASP, Nonterminal, was not found in name map.) (Residue 79: PHE, Nonterminal, was not found in name map.) (Residue 80: PHE, Nonterminal, was not found in name map.) (Residue 81: LYS, Nonterminal, was not found in name map.) (Residue 82: SER, Nonterminal, was not found in name map.) (Residue 83: ALA, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 84 to: CMET. (Residue 85: ME, Terminal/last, was not found in name map.) Unknown residue: ME number: 85 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Mapped residue MET, term: Terminal/last, seq. number: 86 to: CMET. Mapped residue PRO, term: Terminal/beginning, seq. number: 87 to: NPRO. (Residue 88: GLU, Nonterminal, was not found in name map.) (Residue 89: GLY, Nonterminal, was not found in name map.) (Residue 90: TYR, Nonterminal, was not found in name map.) (Residue 91: VAL, Nonterminal, was not found in name map.) (Residue 92: GLN, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: THR, Nonterminal, was not found in name map.) (Residue 96: ILE, Nonterminal, was not found in name map.) (Residue 97: PHE, Nonterminal, was not found in name map.) (Residue 98: PHE, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: ASP, Nonterminal, was not found in name map.) (Residue 101: ASP, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: ASN, Nonterminal, was not found in name map.) (Residue 104: TYR, Nonterminal, was not found in name map.) (Residue 105: LYS, Nonterminal, was not found in name map.) (Residue 106: THR, Nonterminal, was not found in name map.) (Residue 107: ARG, Nonterminal, was not found in name map.) (Residue 108: ALA, Nonterminal, was not found in name map.) (Residue 109: GLU, Nonterminal, was not found in name map.) (Residue 110: VAL, Nonterminal, was not found in name map.) (Residue 111: LYS, Nonterminal, was not found in name map.) (Residue 112: PHE, Nonterminal, was not found in name map.) (Residue 113: GLU, Nonterminal, was not found in name map.) (Residue 114: GLY, Nonterminal, was not found in name map.) (Residue 115: ASP, Nonterminal, was not found in name map.) (Residue 116: THR, Nonterminal, was not found in name map.) (Residue 117: LEU, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: ASN, Nonterminal, was not found in name map.) (Residue 120: ARG, Nonterminal, was not found in name map.) (Residue 121: ILE, Nonterminal, was not found in name map.) (Residue 122: GLU, Nonterminal, was not found in name map.) (Residue 123: LEU, Nonterminal, was not found in name map.) (Residue 124: LYS, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ILE, Nonterminal, was not found in name map.) (Residue 127: ASP, Nonterminal, was not found in name map.) (Residue 128: PHE, Nonterminal, was not found in name map.) (Residue 129: LYS, 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: GLY, Nonterminal, was not found in name map.) (Residue 133: ASN, Nonterminal, was not found in name map.) (Residue 134: ILE, Nonterminal, was not found in name map.) (Residue 135: LEU, Nonterminal, was not found in name map.) (Residue 136: GLY, Nonterminal, was not found in name map.) (Residue 137: HID, Nonterminal, was not found in name map.) (Residue 138: LYS, Nonterminal, was not found in name map.) (Residue 139: LEU, Nonterminal, was not found in name map.) (Residue 140: GLU, Nonterminal, was not found in name map.) (Residue 141: TYR, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) (Residue 143: TYR, Nonterminal, was not found in name map.) (Residue 144: ASN, Nonterminal, was not found in name map.) (Residue 145: SER, Nonterminal, was not found in name map.) (Residue 146: HID, Nonterminal, was not found in name map.) (Residue 147: ASN, Nonterminal, was not found in name map.) (Residue 148: VAL, Nonterminal, was not found in name map.) (Residue 149: TYR, Nonterminal, was not found in name map.) (Residue 150: ILE, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 151 to: CMET. Mapped residue ALA, term: Terminal/beginning, seq. number: 152 to: NALA. (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: LYS, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: LYS, Nonterminal, was not found in name map.) (Residue 157: ASN, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: ILE, Nonterminal, was not found in name map.) (Residue 160: LYS, Nonterminal, was not found in name map.) (Residue 161: VAL, Nonterminal, was not found in name map.) (Residue 162: ASN, Nonterminal, was not found in name map.) (Residue 163: PHE, Nonterminal, was not found in name map.) (Residue 164: LYS, Nonterminal, was not found in name map.) (Residue 165: ILE, Nonterminal, was not found in name map.) (Residue 166: ARG, Nonterminal, was not found in name map.) (Residue 167: HIE, Nonterminal, was not found in name map.) (Residue 168: ASN, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: GLU, Nonterminal, was not found in name map.) (Residue 171: ASP, Nonterminal, was not found in name map.) (Residue 172: GLY, Nonterminal, was not found in name map.) (Residue 173: SER, Nonterminal, was not found in name map.) (Residue 174: VAL, Nonterminal, was not found in name map.) (Residue 175: GLN, Nonterminal, was not found in name map.) (Residue 176: LEU, Nonterminal, was not found in name map.) (Residue 177: ALA, Nonterminal, was not found in name map.) (Residue 178: ASP, Nonterminal, was not found in name map.) (Residue 179: HID, Nonterminal, was not found in name map.) (Residue 180: TYR, Nonterminal, was not found in name map.) (Residue 181: GLN, Nonterminal, was not found in name map.) (Residue 182: GLN, Nonterminal, was not found in name map.) (Residue 183: ASN, Nonterminal, was not found in name map.) (Residue 184: THR, Nonterminal, was not found in name map.) (Residue 185: PRO, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: GLY, Nonterminal, was not found in name map.) (Residue 188: ASP, Nonterminal, was not found in name map.) (Residue 189: GLY, Nonterminal, was not found in name map.) (Residue 190: PRO, Nonterminal, was not found in name map.) (Residue 191: VAL, Nonterminal, was not found in name map.) (Residue 192: LEU, Nonterminal, was not found in name map.) (Residue 193: LEU, Nonterminal, was not found in name map.) (Residue 194: PRO, Nonterminal, was not found in name map.) (Residue 195: ASP, Nonterminal, was not found in name map.) (Residue 196: ASN, Nonterminal, was not found in name map.) (Residue 197: HID, Nonterminal, was not found in name map.) (Residue 198: TYR, Nonterminal, was not found in name map.) (Residue 199: LEU, Nonterminal, was not found in name map.) (Residue 200: SER, Nonterminal, was not found in name map.) (Residue 201: THR, Nonterminal, was not found in name map.) (Residue 202: GLN, Nonterminal, was not found in name map.) (Residue 203: SER, Nonterminal, was not found in name map.) (Residue 204: ALA, Nonterminal, was not found in name map.) (Residue 205: LEU, Nonterminal, was not found in name map.) (Residue 206: SER, Nonterminal, was not found in name map.) (Residue 207: LYS, Nonterminal, was not found in name map.) (Residue 208: ASP, 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: GLU, Nonterminal, was not found in name map.) (Residue 212: LYS, Nonterminal, was not found in name map.) (Residue 213: ARG, Nonterminal, was not found in name map.) (Residue 214: ASP, Nonterminal, was not found in name map.) (Residue 215: HID, Nonterminal, was not found in name map.) Mapped residue MET, term: Terminal/last, seq. number: 216 to: CMET. (Residue 217: ME, Terminal/last, was not found in name map.) Unknown residue: ME number: 217 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Mapped residue MET, term: Terminal/last, seq. number: 218 to: CMET. Mapped residue VAL, term: Terminal/beginning, seq. number: 219 to: NVAL. (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: LEU, Nonterminal, was not found in name map.) (Residue 222: GLU, Nonterminal, was not found in name map.) (Residue 223: PHE, Nonterminal, was not found in name map.) (Residue 224: VAL, Nonterminal, was not found in name map.) (Residue 225: THR, Nonterminal, was not found in name map.) (Residue 226: ALA, Nonterminal, was not found in name map.) (Residue 227: ALA, Nonterminal, was not found in name map.) (Residue 228: GLY, Nonterminal, was not found in name map.) Mapped residue ILE, term: Terminal/last, seq. number: 229 to: CILE. Joining NSER - LYS Joining LYS - GLY Joining GLY - GLU Joining GLU - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - LEU Joining LEU - PHE Joining PHE - THR Joining THR - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - PRO Joining PRO - ILE Joining ILE - LEU Joining LEU - VAL Joining VAL - GLU Joining GLU - LEU Joining LEU - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - VAL Joining VAL - ASN Joining ASN - GLY Joining GLY - HIE Joining HIE - LYS Added missing heavy atom: .R.A Joining LYS - PHE Joining PHE - SER Joining SER - VAL Joining VAL - SER Joining SER - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - GLU Joining GLU - GLY Joining GLY - ASP Joining ASP - ALA Joining ALA - THR Joining THR - TYR Joining TYR - GLY Joining GLY - LYS Joining LYS - LEU Joining LEU - THR Joining THR - LEU Joining LEU - LYS Joining LYS - PHE Joining PHE - ILE Joining ILE - CYS Joining CYS - THR Joining THR - THR Joining THR - GLY Joining GLY - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - LEU Joining LEU - PRO Joining PRO - VAL Joining VAL - PRO Joining PRO - TRP Joining TRP - PRO Joining PRO - THR Joining THR - LEU Joining LEU - VAL Joining VAL - THR Joining THR - THR Joining THR - PHE Joining PHE - CRO Joining NVAL - GLN Joining GLN - CYS Joining CYS - PHE Joining PHE - SER Joining SER - ARG Joining ARG - TYR Joining TYR - PRO Joining PRO - ASP Joining ASP - HIE Joining HIE - CMET Created a new atom named: SE within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NLYS - ARG Joining ARG - HIE Joining HIE - ASP Joining ASP - PHE Joining PHE - PHE Joining PHE - LYS Joining LYS - SER Joining SER - ALA Joining ALA - CMET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: ME sequence: 86 Created a new atom named: SD within residue: .R 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining NPRO - GLU Joining GLU - GLY Joining GLY - TYR Joining TYR - VAL Joining VAL - GLN Joining GLN - GLU Joining GLU - ARG Joining ARG - THR Joining THR - ILE Joining ILE - PHE Joining PHE - PHE Joining PHE - LYS Added missing heavy atom: .R.A Joining LYS - ASP Joining ASP - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - TYR Joining TYR - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - THR Joining THR - ARG Joining ARG - ALA Joining ALA - GLU Joining GLU - VAL Joining VAL - LYS Joining LYS - PHE Joining PHE - GLU Joining GLU - GLY Joining GLY - ASP Joining ASP - THR Joining THR - LEU Joining LEU - 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 Joining ARG - ILE Joining ILE - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - LEU Joining LEU - LYS Joining LYS - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - PHE Joining PHE - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - GLU Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining GLU - ASP Joining ASP - GLY Joining GLY - ASN Joining ASN - ILE Joining ILE - LEU Joining LEU - GLY Joining GLY - HID Joining HID - LYS Joining LYS - LEU Joining LEU - GLU Joining GLU - TYR Joining TYR - ASN Joining ASN - TYR Joining TYR - ASN Joining ASN - SER Joining SER - HID Joining HID - ASN Joining ASN - VAL Joining VAL - TYR Joining TYR - ILE Joining ILE - CMET Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NALA - ASP Joining ASP - 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 - GLN 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 GLN - 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 Added missing heavy atom: .R.A Joining LYS - ASN Joining ASN - GLY Joining GLY - ILE Joining ILE - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - VAL Joining VAL - ASN Joining ASN - PHE Joining PHE - LYS Joining LYS - ILE Joining ILE - ARG Joining ARG - HIE Joining HIE - ASN Joining ASN - ILE Joining ILE - GLU Joining GLU - ASP Joining ASP - GLY Joining GLY - SER Joining SER - VAL Joining VAL - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - ASP Joining ASP - HID Joining HID - TYR Joining TYR - GLN Joining GLN - GLN Joining GLN - ASN Joining ASN - THR Joining THR - PRO Joining PRO - ILE Joining ILE - GLY Joining GLY - ASP Joining ASP - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - LEU Joining LEU - PRO Joining PRO - ASP Joining ASP - ASN Joining ASN - HID Joining HID - TYR Joining TYR - LEU Joining LEU - SER Joining SER - THR Joining THR - GLN Joining GLN - SER Joining SER - ALA Joining ALA - LEU Joining LEU - SER Joining SER - LYS Joining LYS - ASP Joining ASP - PRO Joining PRO - ASN Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining ASN - GLU Joining GLU - LYS Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining LYS - ARG Joining ARG - ASP Joining ASP - HID Joining HID - CMET Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: ME sequence: 218 Created a new atom named: SD within residue: .R 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 Added missing heavy atom: .R.A Added missing heavy atom: .R.A Created a new atom named: H within residue: .R Joining NVAL - LEU Joining LEU - LEU Joining LEU - GLU Joining GLU - PHE Joining PHE - VAL Joining VAL - THR Joining THR - ALA Joining ALA - ALA Joining ALA - GLY Joining GLY - CILE Added missing heavy atom: .R.A total atoms in file: 3440 Leap added 195 missing atoms according to residue templates: 69 Heavy 126 H / lone pairs The file contained 6 atoms not in residue templates > saveAmberParm x gfp.parm7 gfp.rst7 Checking Unit. WARNING: There is a bond of 4.982997 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.615864 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.428284 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 6.282434 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.254820 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.171454 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.659759 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 4.853690 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -7.000003 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