log started: Thu Aug 18 07:51:18 2016 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # ----- this file is updated 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" } > { "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" "Ca" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /lap/amber/12.0.21/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: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) > frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /lap/amber/12.0.21/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /lap/amber/12.0.21/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN > # > # Load main chain and terminating > # amino acid libraries (i.e. ff94 libs) > # > loadOff all_amino94.lib Loading library: /lap/amber/12.0.21/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff all_aminoct94.lib Loading library: /lap/amber/12.0.21/dat/leap/lib/all_aminoct94.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff all_aminont94.lib Loading library: /lap/amber/12.0.21/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > # > # Load water and ions > # > loadOff ions94.lib Loading library: /lap/amber/12.0.21/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: /lap/amber/12.0.21/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: TIP5PBOX 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 > parm = loadamberparams frcmod.known Loading parameters: ./frcmod.known Reading force field modification type file (frcmod) Reading title: Fvisor' for the dihedral termsRCMOD file generated by PyRED version SEP-2015 - q4md-forcefieldtools.org > F02 = loadmol2 F02.mol2 Loading Mol2 file: ./F02.mol2 Reading MOLECULE named F02 > p = loadpdb protein.pdb Loading PDB file: ./protein.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLU, term: Terminal/beginning, seq. number: 0 to: NGLU. (Residue 1: GLY, Nonterminal, was not found in name map.) (Residue 2: ARG, Nonterminal, was not found in name map.) (Residue 3: GLU, Nonterminal, was not found in name map.) (Residue 4: ASP, Nonterminal, was not found in name map.) (Residue 5: PRO, Nonterminal, was not found in name map.) (Residue 6: GLN, Nonterminal, was not found in name map.) (Residue 7: LEU, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: VAL, Nonterminal, was not found in name map.) (Residue 10: ARG, Nonterminal, was not found in name map.) (Residue 11: VAL, Nonterminal, was not found in name map.) (Residue 12: ARG, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: GLY, Nonterminal, was not found in name map.) (Residue 15: GLN, Nonterminal, was not found in name map.) (Residue 16: LEU, Nonterminal, was not found in name map.) (Residue 17: ARG, Nonterminal, was not found in name map.) (Residue 18: GLY, Nonterminal, was not found in name map.) (Residue 19: ILE, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: LYS, Nonterminal, was not found in name map.) (Residue 23: ALA, Nonterminal, was not found in name map.) (Residue 24: PRO, Nonterminal, was not found in name map.) (Residue 25: GLY, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: PRO, Nonterminal, was not found in name map.) (Residue 28: VAL, Nonterminal, was not found in name map.) (Residue 29: SER, Nonterminal, was not found in name map.) (Residue 30: ALA, Nonterminal, was not found in name map.) (Residue 31: PHE, Nonterminal, was not found in name map.) (Residue 32: LEU, Nonterminal, was not found in name map.) (Residue 33: GLY, Nonterminal, was not found in name map.) (Residue 34: ILE, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: PHE, Nonterminal, was not found in name map.) (Residue 37: ALA, Nonterminal, was not found in name map.) (Residue 38: GLU, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: PRO, Nonterminal, was not found in name map.) (Residue 41: VAL, Nonterminal, was not found in name map.) (Residue 42: GLY, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: ARG, Nonterminal, was not found in name map.) (Residue 45: ARG, Nonterminal, was not found in name map.) (Residue 46: PHE, Nonterminal, was not found in name map.) (Residue 47: MET, Nonterminal, was not found in name map.) (Residue 48: PRO, Nonterminal, was not found in name map.) (Residue 49: PRO, Nonterminal, was not found in name map.) (Residue 50: GLU, Nonterminal, was not found in name map.) (Residue 51: PRO, Nonterminal, was not found in name map.) (Residue 52: LYS, Nonterminal, was not found in name map.) (Residue 53: ARG, 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: SER, Nonterminal, was not found in name map.) (Residue 57: GLY, Nonterminal, was not found in name map.) (Residue 58: VAL, Nonterminal, was not found in name map.) (Residue 59: LEU, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: ALA, Nonterminal, was not found in name map.) (Residue 62: THR, Nonterminal, was not found in name map.) (Residue 63: THR, Nonterminal, was not found in name map.) (Residue 64: PHE, Nonterminal, was not found in name map.) (Residue 65: GLN, Nonterminal, was not found in name map.) (Residue 66: ASN, Nonterminal, was not found in name map.) (Residue 67: VAL, Nonterminal, was not found in name map.) (Residue 68: CYX, Nonterminal, was not found in name map.) (Residue 69: TYR, Nonterminal, was not found in name map.) (Residue 70: GLN, Nonterminal, was not found in name map.) (Residue 71: TYR, Nonterminal, was not found in name map.) (Residue 72: VAL, Nonterminal, was not found in name map.) (Residue 73: ASP, Nonterminal, was not found in name map.) (Residue 74: THR, Nonterminal, was not found in name map.) (Residue 75: LEU, Nonterminal, was not found in name map.) (Residue 76: TYR, Nonterminal, was not found in name map.) (Residue 77: PRO, Nonterminal, was not found in name map.) (Residue 78: GLY, Nonterminal, was not found in name map.) (Residue 79: PHE, Nonterminal, was not found in name map.) (Residue 80: GLU, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: THR, Nonterminal, was not found in name map.) (Residue 83: GLU, Nonterminal, was not found in name map.) (Residue 84: MET, Nonterminal, was not found in name map.) (Residue 85: TRP, Nonterminal, was not found in name map.) (Residue 86: ASN, Nonterminal, was not found in name map.) (Residue 87: PRO, Nonterminal, was not found in name map.) (Residue 88: ASN, Nonterminal, was not found in name map.) (Residue 89: ARG, Nonterminal, was not found in name map.) (Residue 90: GLU, Nonterminal, was not found in name map.) (Residue 91: LEU, Nonterminal, was not found in name map.) (Residue 92: SER, Nonterminal, was not found in name map.) (Residue 93: GLU, Nonterminal, was not found in name map.) (Residue 94: ASP, Nonterminal, was not found in name map.) (Residue 95: CYX, Nonterminal, was not found in name map.) (Residue 96: LEU, Nonterminal, was not found in name map.) (Residue 97: TYR, Nonterminal, was not found in name map.) (Residue 98: LEU, Nonterminal, was not found in name map.) (Residue 99: ASN, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: TRP, Nonterminal, was not found in name map.) (Residue 102: THR, Nonterminal, was not found in name map.) (Residue 103: PRO, Nonterminal, was not found in name map.) (Residue 104: TYR, Nonterminal, was not found in name map.) (Residue 105: PRO, Nonterminal, was not found in name map.) (Residue 106: ARG, Nonterminal, was not found in name map.) (Residue 107: PRO, Nonterminal, was not found in name map.) (Residue 108: ALA, Nonterminal, was not found in name map.) (Residue 109: SER, Nonterminal, was not found in name map.) (Residue 110: PRO, Nonterminal, was not found in name map.) (Residue 111: THR, Nonterminal, was not found in name map.) (Residue 112: PRO, Nonterminal, was not found in name map.) (Residue 113: VAL, Nonterminal, was not found in name map.) (Residue 114: LEU, Nonterminal, was not found in name map.) (Residue 115: ILE, Nonterminal, was not found in name map.) (Residue 116: TRP, Nonterminal, was not found in name map.) (Residue 117: ILE, Nonterminal, was not found in name map.) (Residue 118: TYR, Nonterminal, was not found in name map.) (Residue 119: GLY, Nonterminal, was not found in name map.) (Residue 120: GLY, Nonterminal, was not found in name map.) (Residue 121: GLY, Nonterminal, was not found in name map.) (Residue 122: PHE, Nonterminal, was not found in name map.) (Residue 123: TYR, Nonterminal, was not found in name map.) (Residue 124: SER, Nonterminal, was not found in name map.) (Residue 125: GLY, Nonterminal, was not found in name map.) (Residue 126: ALA, Nonterminal, was not found in name map.) (Residue 127: ALA, Nonterminal, was not found in name map.) (Residue 128: SER, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: ASP, Nonterminal, was not found in name map.) (Residue 131: VAL, Nonterminal, was not found in name map.) (Residue 132: TYR, Nonterminal, was not found in name map.) (Residue 133: ASP, Nonterminal, was not found in name map.) (Residue 134: GLY, Nonterminal, was not found in name map.) (Residue 135: ARG, Nonterminal, was not found in name map.) (Residue 136: PHE, Nonterminal, was not found in name map.) (Residue 137: LEU, Nonterminal, was not found in name map.) (Residue 138: ALA, Nonterminal, was not found in name map.) (Residue 139: GLN, Nonterminal, was not found in name map.) (Residue 140: VAL, Nonterminal, was not found in name map.) (Residue 141: GLU, Nonterminal, was not found in name map.) (Residue 142: GLY, Nonterminal, was not found in name map.) (Residue 143: ALA, Nonterminal, was not found in name map.) (Residue 144: VAL, Nonterminal, was not found in name map.) (Residue 145: LEU, Nonterminal, was not found in name map.) (Residue 146: VAL, Nonterminal, was not found in name map.) (Residue 147: SER, Nonterminal, was not found in name map.) (Residue 148: MET, Nonterminal, was not found in name map.) (Residue 149: ASN, Nonterminal, was not found in name map.) (Residue 150: TYR, Nonterminal, was not found in name map.) (Residue 151: ARG, Nonterminal, was not found in name map.) (Residue 152: VAL, Nonterminal, was not found in name map.) (Residue 153: GLY, Nonterminal, was not found in name map.) (Residue 154: THR, Nonterminal, was not found in name map.) (Residue 155: PHE, Nonterminal, was not found in name map.) (Residue 156: GLY, Nonterminal, was not found in name map.) (Residue 157: PHE, Nonterminal, was not found in name map.) (Residue 158: LEU, Nonterminal, was not found in name map.) (Residue 159: ALA, Nonterminal, was not found in name map.) (Residue 160: LEU, Nonterminal, was not found in name map.) (Residue 161: PRO, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: SER, Nonterminal, was not found in name map.) (Residue 164: ARG, Nonterminal, was not found in name map.) (Residue 165: GLU, Nonterminal, was not found in name map.) (Residue 166: ALA, Nonterminal, was not found in name map.) (Residue 167: PRO, Nonterminal, was not found in name map.) (Residue 168: GLY, Nonterminal, was not found in name map.) (Residue 169: ASN, Nonterminal, was not found in name map.) (Residue 170: VAL, Nonterminal, was not found in name map.) (Residue 171: GLY, Nonterminal, was not found in name map.) (Residue 172: LEU, Nonterminal, was not found in name map.) (Residue 173: LEU, Nonterminal, was not found in name map.) (Residue 174: ASP, Nonterminal, was not found in name map.) (Residue 175: GLN, Nonterminal, was not found in name map.) (Residue 176: ARG, Nonterminal, was not found in name map.) (Residue 177: LEU, Nonterminal, was not found in name map.) (Residue 178: ALA, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: GLN, Nonterminal, was not found in name map.) (Residue 181: TRP, Nonterminal, was not found in name map.) (Residue 182: VAL, Nonterminal, was not found in name map.) (Residue 183: GLN, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) (Residue 185: ASN, Nonterminal, was not found in name map.) (Residue 186: ILE, Nonterminal, was not found in name map.) (Residue 187: ALA, Nonterminal, was not found in name map.) (Residue 188: ALA, Nonterminal, was not found in name map.) (Residue 189: PHE, Nonterminal, was not found in name map.) (Residue 190: GLY, Nonterminal, was not found in name map.) (Residue 191: GLY, Nonterminal, was not found in name map.) (Residue 192: ASP, Nonterminal, was not found in name map.) (Residue 193: PRO, Nonterminal, was not found in name map.) (Residue 194: MET, Nonterminal, was not found in name map.) (Residue 195: SER, Nonterminal, was not found in name map.) (Residue 196: VAL, Nonterminal, was not found in name map.) (Residue 197: THR, Nonterminal, was not found in name map.) (Residue 198: LEU, Nonterminal, was not found in name map.) (Residue 199: PHE, Nonterminal, was not found in name map.) (Residue 200: GLY, Nonterminal, was not found in name map.) (Residue 201: GLU, Nonterminal, was not found in name map.) (Residue 202: F02, Nonterminal, was not found in name map.) (Residue 203: ALA, Nonterminal, was not found in name map.) (Residue 204: GLY, Nonterminal, was not found in name map.) (Residue 205: ALA, Nonterminal, was not found in name map.) (Residue 206: ALA, Nonterminal, was not found in name map.) (Residue 207: SER, Nonterminal, was not found in name map.) (Residue 208: VAL, Nonterminal, was not found in name map.) (Residue 209: GLY, Nonterminal, was not found in name map.) (Residue 210: MET, Nonterminal, was not found in name map.) (Residue 211: HIS, Nonterminal, was not found in name map.) (Residue 212: ILE, Nonterminal, was not found in name map.) (Residue 213: LEU, Nonterminal, was not found in name map.) (Residue 214: SER, Nonterminal, was not found in name map.) (Residue 215: LEU, Nonterminal, was not found in name map.) (Residue 216: PRO, Nonterminal, was not found in name map.) (Residue 217: SER, Nonterminal, was not found in name map.) (Residue 218: ARG, Nonterminal, was not found in name map.) (Residue 219: SER, Nonterminal, was not found in name map.) (Residue 220: LEU, Nonterminal, was not found in name map.) (Residue 221: PHE, Nonterminal, was not found in name map.) (Residue 222: HIS, Nonterminal, was not found in name map.) (Residue 223: ARG, Nonterminal, was not found in name map.) (Residue 224: ALA, Nonterminal, was not found in name map.) (Residue 225: VAL, Nonterminal, was not found in name map.) (Residue 226: LEU, Nonterminal, was not found in name map.) (Residue 227: GLN, Nonterminal, was not found in name map.) (Residue 228: SER, Nonterminal, was not found in name map.) (Residue 229: GLY, Nonterminal, was not found in name map.) (Residue 230: THR, Nonterminal, was not found in name map.) (Residue 231: PRO, Nonterminal, was not found in name map.) (Residue 232: ASN, Nonterminal, was not found in name map.) (Residue 233: GLY, Nonterminal, was not found in name map.) (Residue 234: PRO, Nonterminal, was not found in name map.) (Residue 235: TRP, Nonterminal, was not found in name map.) (Residue 236: ALA, Nonterminal, was not found in name map.) (Residue 237: THR, Nonterminal, was not found in name map.) (Residue 238: VAL, Nonterminal, was not found in name map.) (Residue 239: SER, Nonterminal, was not found in name map.) (Residue 240: ALA, Nonterminal, was not found in name map.) (Residue 241: GLY, Nonterminal, was not found in name map.) (Residue 242: GLU, Nonterminal, was not found in name map.) (Residue 243: ALA, Nonterminal, was not found in name map.) (Residue 244: ARG, Nonterminal, was not found in name map.) (Residue 245: ARG, Nonterminal, was not found in name map.) (Residue 246: ARG, Nonterminal, was not found in name map.) (Residue 247: ALA, Nonterminal, was not found in name map.) (Residue 248: THR, Nonterminal, was not found in name map.) (Residue 249: LEU, Nonterminal, was not found in name map.) (Residue 250: LEU, Nonterminal, was not found in name map.) (Residue 251: ALA, Nonterminal, was not found in name map.) (Residue 252: ARG, Nonterminal, was not found in name map.) (Residue 253: LEU, Nonterminal, was not found in name map.) (Residue 254: VAL, Nonterminal, was not found in name map.) (Residue 255: GLY, Nonterminal, was not found in name map.) (Residue 256: CYX, Nonterminal, was not found in name map.) (Residue 257: PRO, Nonterminal, was not found in name map.) (Residue 258: PRO, Nonterminal, was not found in name map.) (Residue 259: GLY, Nonterminal, was not found in name map.) (Residue 260: GLY, Nonterminal, was not found in name map.) (Residue 261: ALA, Nonterminal, was not found in name map.) (Residue 262: GLY, Nonterminal, was not found in name map.) (Residue 263: GLY, Nonterminal, was not found in name map.) (Residue 264: ASN, Nonterminal, was not found in name map.) (Residue 265: ASP, Nonterminal, was not found in name map.) (Residue 266: THR, Nonterminal, was not found in name map.) (Residue 267: GLU, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: ILE, Nonterminal, was not found in name map.) (Residue 270: ALA, Nonterminal, was not found in name map.) (Residue 271: CYX, Nonterminal, was not found in name map.) (Residue 272: LEU, Nonterminal, was not found in name map.) (Residue 273: ARG, Nonterminal, was not found in name map.) (Residue 274: THR, Nonterminal, was not found in name map.) (Residue 275: ARG, Nonterminal, was not found in name map.) (Residue 276: PRO, Nonterminal, was not found in name map.) (Residue 277: ALA, Nonterminal, was not found in name map.) (Residue 278: GLN, Nonterminal, was not found in name map.) (Residue 279: ASP, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: VAL, Nonterminal, was not found in name map.) (Residue 282: ASP, Nonterminal, was not found in name map.) (Residue 283: HIS, Nonterminal, was not found in name map.) (Residue 284: GLU, Nonterminal, was not found in name map.) (Residue 285: TRP, Nonterminal, was not found in name map.) (Residue 286: HIS, Nonterminal, was not found in name map.) (Residue 287: VAL, Nonterminal, was not found in name map.) (Residue 288: LEU, Nonterminal, was not found in name map.) (Residue 289: PRO, Nonterminal, was not found in name map.) (Residue 290: GLN, Nonterminal, was not found in name map.) (Residue 291: GLU, Nonterminal, was not found in name map.) (Residue 292: SER, Nonterminal, was not found in name map.) (Residue 293: ILE, Nonterminal, was not found in name map.) (Residue 294: PHE, Nonterminal, was not found in name map.) (Residue 295: ARG, Nonterminal, was not found in name map.) (Residue 296: PHE, Nonterminal, was not found in name map.) (Residue 297: SER, Nonterminal, was not found in name map.) (Residue 298: PHE, Nonterminal, was not found in name map.) (Residue 299: VAL, Nonterminal, was not found in name map.) (Residue 300: PRO, Nonterminal, was not found in name map.) (Residue 301: VAL, Nonterminal, was not found in name map.) (Residue 302: VAL, Nonterminal, was not found in name map.) (Residue 303: ASP, Nonterminal, was not found in name map.) (Residue 304: GLY, Nonterminal, was not found in name map.) (Residue 305: ASP, Nonterminal, was not found in name map.) (Residue 306: PHE, Nonterminal, was not found in name map.) (Residue 307: LEU, Nonterminal, was not found in name map.) (Residue 308: SER, Nonterminal, was not found in name map.) (Residue 309: ASP, Nonterminal, was not found in name map.) (Residue 310: THR, Nonterminal, was not found in name map.) (Residue 311: PRO, Nonterminal, was not found in name map.) (Residue 312: GLU, Nonterminal, was not found in name map.) (Residue 313: ALA, Nonterminal, was not found in name map.) (Residue 314: LEU, Nonterminal, was not found in name map.) (Residue 315: ILE, Nonterminal, was not found in name map.) (Residue 316: ASN, Nonterminal, was not found in name map.) (Residue 317: THR, Nonterminal, was not found in name map.) (Residue 318: GLY, Nonterminal, was not found in name map.) (Residue 319: ASP, Nonterminal, was not found in name map.) (Residue 320: PHE, Nonterminal, was not found in name map.) (Residue 321: GLN, Nonterminal, was not found in name map.) (Residue 322: ASP, Nonterminal, was not found in name map.) (Residue 323: LEU, Nonterminal, was not found in name map.) (Residue 324: GLN, Nonterminal, was not found in name map.) (Residue 325: VAL, Nonterminal, was not found in name map.) (Residue 326: LEU, Nonterminal, was not found in name map.) (Residue 327: VAL, Nonterminal, was not found in name map.) (Residue 328: GLY, Nonterminal, was not found in name map.) (Residue 329: VAL, Nonterminal, was not found in name map.) (Residue 330: VAL, Nonterminal, was not found in name map.) (Residue 331: LYS, Nonterminal, was not found in name map.) (Residue 332: ASP, Nonterminal, was not found in name map.) (Residue 333: GLU, Nonterminal, was not found in name map.) (Residue 334: GLY, Nonterminal, was not found in name map.) (Residue 335: SER, Nonterminal, was not found in name map.) (Residue 336: TYR, Nonterminal, was not found in name map.) (Residue 337: PHE, Nonterminal, was not found in name map.) (Residue 338: LEU, Nonterminal, was not found in name map.) (Residue 339: VAL, Nonterminal, was not found in name map.) (Residue 340: TYR, Nonterminal, was not found in name map.) (Residue 341: GLY, Nonterminal, was not found in name map.) (Residue 342: VAL, Nonterminal, was not found in name map.) (Residue 343: PRO, Nonterminal, was not found in name map.) (Residue 344: GLY, Nonterminal, was not found in name map.) (Residue 345: PHE, Nonterminal, was not found in name map.) (Residue 346: SER, Nonterminal, was not found in name map.) (Residue 347: LYS, Nonterminal, was not found in name map.) (Residue 348: ASP, Nonterminal, was not found in name map.) (Residue 349: ASN, Nonterminal, was not found in name map.) (Residue 350: GLU, Nonterminal, was not found in name map.) (Residue 351: SER, Nonterminal, was not found in name map.) (Residue 352: LEU, Nonterminal, was not found in name map.) (Residue 353: ILE, Nonterminal, was not found in name map.) (Residue 354: SER, Nonterminal, was not found in name map.) (Residue 355: ARG, Nonterminal, was not found in name map.) (Residue 356: ALA, Nonterminal, was not found in name map.) (Residue 357: GLN, Nonterminal, was not found in name map.) (Residue 358: PHE, Nonterminal, was not found in name map.) (Residue 359: LEU, Nonterminal, was not found in name map.) (Residue 360: ALA, Nonterminal, was not found in name map.) (Residue 361: GLY, Nonterminal, was not found in name map.) (Residue 362: VAL, Nonterminal, was not found in name map.) (Residue 363: ARG, Nonterminal, was not found in name map.) (Residue 364: ILE, Nonterminal, was not found in name map.) (Residue 365: GLY, Nonterminal, was not found in name map.) (Residue 366: VAL, Nonterminal, was not found in name map.) (Residue 367: PRO, Nonterminal, was not found in name map.) (Residue 368: GLN, Nonterminal, was not found in name map.) (Residue 369: ALA, Nonterminal, was not found in name map.) (Residue 370: SER, Nonterminal, was not found in name map.) (Residue 371: ASP, Nonterminal, was not found in name map.) (Residue 372: LEU, Nonterminal, was not found in name map.) (Residue 373: ALA, Nonterminal, was not found in name map.) (Residue 374: ALA, Nonterminal, was not found in name map.) (Residue 375: GLU, Nonterminal, was not found in name map.) (Residue 376: ALA, Nonterminal, was not found in name map.) (Residue 377: VAL, Nonterminal, was not found in name map.) (Residue 378: VAL, Nonterminal, was not found in name map.) (Residue 379: LEU, Nonterminal, was not found in name map.) (Residue 380: HIS, Nonterminal, was not found in name map.) (Residue 381: TYR, Nonterminal, was not found in name map.) (Residue 382: THR, Nonterminal, was not found in name map.) (Residue 383: ASP, Nonterminal, was not found in name map.) (Residue 384: TRP, Nonterminal, was not found in name map.) (Residue 385: LEU, Nonterminal, was not found in name map.) (Residue 386: HIS, Nonterminal, was not found in name map.) (Residue 387: PRO, Nonterminal, was not found in name map.) (Residue 388: GLU, Nonterminal, was not found in name map.) (Residue 389: ASP, Nonterminal, was not found in name map.) (Residue 390: PRO, Nonterminal, was not found in name map.) (Residue 391: THR, Nonterminal, was not found in name map.) (Residue 392: HIS, Nonterminal, was not found in name map.) (Residue 393: LEU, Nonterminal, was not found in name map.) (Residue 394: ARG, Nonterminal, was not found in name map.) (Residue 395: ASP, Nonterminal, was not found in name map.) (Residue 396: ALA, Nonterminal, was not found in name map.) (Residue 397: MET, Nonterminal, was not found in name map.) (Residue 398: SER, Nonterminal, was not found in name map.) (Residue 399: ALA, Nonterminal, was not found in name map.) (Residue 400: VAL, Nonterminal, was not found in name map.) (Residue 401: VAL, Nonterminal, was not found in name map.) (Residue 402: GLY, Nonterminal, was not found in name map.) (Residue 403: ASP, Nonterminal, was not found in name map.) (Residue 404: HIS, Nonterminal, was not found in name map.) (Residue 405: ASN, Nonterminal, was not found in name map.) (Residue 406: VAL, Nonterminal, was not found in name map.) (Residue 407: VAL, Nonterminal, was not found in name map.) (Residue 408: CYX, Nonterminal, was not found in name map.) (Residue 409: PRO, Nonterminal, was not found in name map.) (Residue 410: VAL, Nonterminal, was not found in name map.) (Residue 411: ALA, Nonterminal, was not found in name map.) (Residue 412: GLN, Nonterminal, was not found in name map.) (Residue 413: LEU, Nonterminal, was not found in name map.) (Residue 414: ALA, Nonterminal, was not found in name map.) (Residue 415: GLY, Nonterminal, was not found in name map.) (Residue 416: ARG, Nonterminal, was not found in name map.) (Residue 417: LEU, Nonterminal, was not found in name map.) (Residue 418: ALA, Nonterminal, was not found in name map.) (Residue 419: ALA, Nonterminal, was not found in name map.) (Residue 420: GLN, Nonterminal, was not found in name map.) (Residue 421: GLY, Nonterminal, was not found in name map.) (Residue 422: ALA, Nonterminal, was not found in name map.) (Residue 423: ARG, Nonterminal, was not found in name map.) (Residue 424: VAL, Nonterminal, was not found in name map.) (Residue 425: TYR, Nonterminal, was not found in name map.) (Residue 426: ALA, Nonterminal, was not found in name map.) (Residue 427: TYR, Nonterminal, was not found in name map.) (Residue 428: ILE, Nonterminal, was not found in name map.) (Residue 429: PHE, Nonterminal, was not found in name map.) (Residue 430: GLU, Nonterminal, was not found in name map.) (Residue 431: HIS, Nonterminal, was not found in name map.) (Residue 432: ARG, Nonterminal, was not found in name map.) (Residue 433: ALA, Nonterminal, was not found in name map.) (Residue 434: SER, Nonterminal, was not found in name map.) (Residue 435: THR, Nonterminal, was not found in name map.) (Residue 436: LEU, Nonterminal, was not found in name map.) (Residue 437: THR, Nonterminal, was not found in name map.) (Residue 438: TRP, Nonterminal, was not found in name map.) (Residue 439: PRO, Nonterminal, was not found in name map.) (Residue 440: LEU, Nonterminal, was not found in name map.) (Residue 441: TRP, Nonterminal, was not found in name map.) (Residue 442: MET, Nonterminal, was not found in name map.) (Residue 443: GLY, Nonterminal, was not found in name map.) (Residue 444: VAL, Nonterminal, was not found in name map.) (Residue 445: PRO, Nonterminal, was not found in name map.) (Residue 446: HIS, Nonterminal, was not found in name map.) (Residue 447: GLY, Nonterminal, was not found in name map.) (Residue 448: TYR, Nonterminal, was not found in name map.) (Residue 449: GLU, Nonterminal, was not found in name map.) (Residue 450: ILE, Nonterminal, was not found in name map.) (Residue 451: GLU, Nonterminal, was not found in name map.) (Residue 452: PHE, Nonterminal, was not found in name map.) (Residue 453: ILE, Nonterminal, was not found in name map.) (Residue 454: PHE, Nonterminal, was not found in name map.) (Residue 455: GLY, Nonterminal, was not found in name map.) (Residue 456: LEU, Nonterminal, was not found in name map.) (Residue 457: PRO, Nonterminal, was not found in name map.) (Residue 458: LEU, Nonterminal, was not found in name map.) (Residue 459: ASP, Nonterminal, was not found in name map.) (Residue 460: PRO, Nonterminal, was not found in name map.) (Residue 461: SER, Nonterminal, was not found in name map.) (Residue 462: LEU, Nonterminal, was not found in name map.) (Residue 463: ASN, Nonterminal, was not found in name map.) (Residue 464: TYR, Nonterminal, was not found in name map.) (Residue 465: THR, Nonterminal, was not found in name map.) (Residue 466: THR, Nonterminal, was not found in name map.) (Residue 467: GLU, Nonterminal, was not found in name map.) (Residue 468: GLU, Nonterminal, was not found in name map.) (Residue 469: ARG, Nonterminal, was not found in name map.) (Residue 470: ILE, Nonterminal, was not found in name map.) (Residue 471: PHE, Nonterminal, was not found in name map.) (Residue 472: ALA, Nonterminal, was not found in name map.) (Residue 473: GLN, Nonterminal, was not found in name map.) (Residue 474: ARG, Nonterminal, was not found in name map.) (Residue 475: LEU, Nonterminal, was not found in name map.) (Residue 476: MET, Nonterminal, was not found in name map.) (Residue 477: LYS, Nonterminal, was not found in name map.) (Residue 478: TYR, Nonterminal, was not found in name map.) (Residue 479: TRP, Nonterminal, was not found in name map.) (Residue 480: THR, Nonterminal, was not found in name map.) (Residue 481: ASN, Nonterminal, was not found in name map.) (Residue 482: PHE, Nonterminal, was not found in name map.) (Residue 483: ALA, Nonterminal, was not found in name map.) (Residue 484: ARG, Nonterminal, was not found in name map.) (Residue 485: THR, Nonterminal, was not found in name map.) (Residue 486: GLY, Nonterminal, was not found in name map.) (Residue 487: ASP, Nonterminal, was not found in name map.) (Residue 488: PRO, Nonterminal, was not found in name map.) (Residue 489: ASN, Nonterminal, was not found in name map.) (Residue 490: ASP, Nonterminal, was not found in name map.) (Residue 491: PRO, Nonterminal, was not found in name map.) (Residue 492: ARG, Nonterminal, was not found in name map.) (Residue 493: ASP, Nonterminal, was not found in name map.) (Residue 494: SER, Nonterminal, was not found in name map.) (Residue 495: LYS, Nonterminal, was not found in name map.) (Residue 496: SER, Nonterminal, was not found in name map.) (Residue 497: PRO, Nonterminal, was not found in name map.) (Residue 498: GLN, Nonterminal, was not found in name map.) (Residue 499: TRP, Nonterminal, was not found in name map.) (Residue 500: PRO, Nonterminal, was not found in name map.) (Residue 501: PRO, Nonterminal, was not found in name map.) (Residue 502: TYR, Nonterminal, was not found in name map.) (Residue 503: THR, Nonterminal, was not found in name map.) (Residue 504: THR, Nonterminal, was not found in name map.) (Residue 505: ALA, Nonterminal, was not found in name map.) (Residue 506: ALA, Nonterminal, was not found in name map.) (Residue 507: GLN, Nonterminal, was not found in name map.) (Residue 508: GLN, Nonterminal, was not found in name map.) (Residue 509: TYR, Nonterminal, was not found in name map.) (Residue 510: VAL, Nonterminal, was not found in name map.) (Residue 511: SER, Nonterminal, was not found in name map.) (Residue 512: LEU, Nonterminal, was not found in name map.) (Residue 513: ASN, Nonterminal, was not found in name map.) (Residue 514: LEU, Nonterminal, was not found in name map.) (Residue 515: LYS, Nonterminal, was not found in name map.) (Residue 516: PRO, Nonterminal, was not found in name map.) (Residue 517: LEU, Nonterminal, was not found in name map.) (Residue 518: GLU, Nonterminal, was not found in name map.) (Residue 519: VAL, Nonterminal, was not found in name map.) (Residue 520: ARG, Nonterminal, was not found in name map.) (Residue 521: ARG, Nonterminal, was not found in name map.) (Residue 522: GLY, Nonterminal, was not found in name map.) (Residue 523: LEU, Nonterminal, was not found in name map.) (Residue 524: ARG, Nonterminal, was not found in name map.) (Residue 525: ALA, Nonterminal, was not found in name map.) (Residue 526: GLN, Nonterminal, was not found in name map.) (Residue 527: THR, Nonterminal, was not found in name map.) (Residue 528: CYX, Nonterminal, was not found in name map.) (Residue 529: ALA, Nonterminal, was not found in name map.) (Residue 530: PHE, Nonterminal, was not found in name map.) (Residue 531: TRP, Nonterminal, was not found in name map.) (Residue 532: ASN, Nonterminal, was not found in name map.) (Residue 533: ARG, Nonterminal, was not found in name map.) (Residue 534: PHE, Nonterminal, was not found in name map.) (Residue 535: LEU, Nonterminal, was not found in name map.) (Residue 536: PRO, Nonterminal, was not found in name map.) (Residue 537: LYS, Nonterminal, was not found in name map.) (Residue 538: LEU, Nonterminal, was not found in name map.) (Residue 539: LEU, Nonterminal, was not found in name map.) (Residue 540: SER, Nonterminal, was not found in name map.) (Residue 541: ALA, Nonterminal, was not found in name map.) Mapped residue THR, term: Terminal/last, seq. number: 542 to: CTHR. Joining NGLU - GLY Joining GLY - ARG Joining ARG - GLU Joining GLU - ASP Joining ASP - PRO Joining PRO - GLN Joining GLN - LEU Joining LEU - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - VAL Joining VAL - ARG Joining ARG - GLY Joining GLY - GLY Joining GLY - GLN Joining GLN - LEU Joining LEU - ARG Joining ARG - GLY Joining GLY - ILE Joining ILE - ARG Joining ARG - LEU Joining LEU - LYS Joining LYS - ALA Joining ALA - PRO Joining PRO - GLY Joining GLY - GLY Joining GLY - PRO Joining PRO - VAL Joining VAL - SER Joining SER - ALA Joining ALA - PHE Joining PHE - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PRO Joining PRO - PHE Joining PHE - ALA Joining ALA - GLU Joining GLU - PRO Joining PRO - PRO Joining PRO - VAL Joining VAL - GLY Joining GLY - SER Joining SER - ARG Joining ARG - ARG Joining ARG - PHE Joining PHE - MET Joining MET - PRO Joining PRO - PRO Joining PRO - GLU Joining GLU - PRO Joining PRO - LYS Joining LYS - ARG Joining ARG - PRO Joining PRO - TRP Joining TRP - SER Joining SER - GLY Joining GLY - VAL Joining VAL - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - THR Joining THR - THR Joining THR - PHE Joining PHE - GLN Joining GLN - ASN Joining ASN - VAL Joining VAL - CYX Joining CYX - TYR Joining TYR - GLN Joining GLN - TYR Joining TYR - VAL Joining VAL - ASP Joining ASP - THR Joining THR - LEU Joining LEU - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - GLU Joining GLU - GLY Joining GLY - THR Joining THR - GLU Joining GLU - MET Joining MET - TRP Joining TRP - ASN Joining ASN - PRO Joining PRO - ASN Joining ASN - ARG Joining ARG - GLU Joining GLU - LEU Joining LEU - SER Joining SER - GLU Joining GLU - ASP Joining ASP - CYX Joining CYX - LEU Joining LEU - TYR Joining TYR - LEU Joining LEU - ASN Joining ASN - VAL Joining VAL - TRP Joining TRP - THR Joining THR - PRO Joining PRO - TYR Joining TYR - PRO Joining PRO - ARG Joining ARG - PRO Joining PRO - ALA Joining ALA - SER Joining SER - PRO Joining PRO - THR Joining THR - PRO Joining PRO - VAL Joining VAL - LEU Joining LEU - ILE Joining ILE - TRP Joining TRP - ILE Joining ILE - TYR Joining TYR - GLY Joining GLY - GLY Joining GLY - GLY Joining GLY - PHE Joining PHE - TYR Joining TYR - SER Joining SER - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LEU Joining LEU - ASP Joining ASP - VAL Joining VAL - TYR Joining TYR - ASP Joining ASP - GLY Joining GLY - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLN Joining GLN - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - SER Joining SER - MET Joining MET - ASN Joining ASN - TYR Joining TYR - ARG Joining ARG - VAL Joining VAL - GLY Joining GLY - THR Joining THR - PHE Joining PHE - GLY Joining GLY - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - PRO Joining PRO - GLY Joining GLY - SER Joining SER - ARG Joining ARG - GLU Joining GLU - ALA Joining ALA - PRO Joining PRO - GLY Joining GLY - ASN Joining ASN - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - LEU Joining LEU - ASP Joining ASP - GLN Joining GLN - ARG Joining ARG - LEU Joining LEU - ALA Joining ALA - LEU Joining LEU - GLN Joining GLN - TRP Joining TRP - VAL Joining VAL - GLN Joining GLN - GLU Joining GLU - ASN Joining ASN - ILE Joining ILE - ALA Joining ALA - ALA Joining ALA - PHE Joining PHE - GLY Joining GLY - GLY Joining GLY - ASP Joining ASP - PRO Joining PRO - MET Joining MET - SER Joining SER - VAL Joining VAL - THR Joining THR - LEU Joining LEU - PHE Joining PHE - GLY Joining GLY - GLU Joining GLU - F02 Joining F02 - ALA Joining ALA - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - SER Joining SER - VAL Joining VAL - GLY Joining GLY - MET Joining MET - HIE Joining HIE - ILE Joining ILE - LEU Joining LEU - SER Joining SER - LEU Joining LEU - PRO Joining PRO - SER Joining SER - ARG Joining ARG - SER Joining SER - LEU Joining LEU - PHE Joining PHE - HIE Joining HIE - ARG Joining ARG - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - SER Joining SER - GLY Joining GLY - THR Joining THR - PRO Joining PRO - ASN Joining ASN - GLY Joining GLY - PRO Joining PRO - TRP Joining TRP - ALA Joining ALA - THR Joining THR - VAL Joining VAL - SER Joining SER - ALA Joining ALA - GLY Joining GLY - GLU Joining GLU - ALA Joining ALA - ARG Joining ARG - ARG Joining ARG - ARG Joining ARG - ALA Joining ALA - THR Joining THR - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - ARG Joining ARG - LEU Joining LEU - VAL Joining VAL - GLY Joining GLY - CYX Joining CYX - PRO Joining PRO - PRO Joining PRO - GLY Joining GLY - GLY Joining GLY - ALA Joining ALA - GLY Joining GLY - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - THR Joining THR - GLU Joining GLU - LEU Joining LEU - ILE Joining ILE - ALA Joining ALA - CYX Joining CYX - LEU Joining LEU - ARG Joining ARG - THR Joining THR - ARG Joining ARG - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - ASP Joining ASP - LEU Joining LEU - VAL Joining VAL - ASP Joining ASP - HIE Joining HIE - GLU Joining GLU - TRP Joining TRP - HIE Joining HIE - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - GLN Joining GLN - GLU Joining GLU - SER Joining SER - ILE Joining ILE - PHE Joining PHE - ARG Joining ARG - PHE Joining PHE - SER Joining SER - PHE Joining PHE - VAL Joining VAL - PRO Joining PRO - VAL Joining VAL - VAL Joining VAL - ASP Joining ASP - GLY Joining GLY - ASP Joining ASP - PHE Joining PHE - LEU Joining LEU - SER Joining SER - ASP Joining ASP - THR Joining THR - PRO Joining PRO - GLU Joining GLU - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - ASN Joining ASN - THR Joining THR - GLY Joining GLY - ASP Joining ASP - PHE Joining PHE - GLN Joining GLN - ASP Joining ASP - LEU Joining LEU - GLN Joining GLN - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - GLY Joining GLY - VAL Joining VAL - VAL Joining VAL - LYS Joining LYS - ASP Joining ASP - GLU Joining GLU - GLY Joining GLY - SER Joining SER - TYR Joining TYR - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - TYR Joining TYR - GLY Joining GLY - VAL Joining VAL - PRO Joining PRO - GLY Joining GLY - PHE Joining PHE - SER Joining SER - LYS Joining LYS - ASP Joining ASP - ASN Joining ASN - GLU Joining GLU - SER Joining SER - LEU Joining LEU - ILE Joining ILE - SER Joining SER - ARG Joining ARG - ALA Joining ALA - GLN Joining GLN - PHE Joining PHE - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - VAL Joining VAL - ARG Joining ARG - ILE Joining ILE - GLY Joining GLY - VAL Joining VAL - PRO Joining PRO - GLN Joining GLN - ALA Joining ALA - SER Joining SER - ASP Joining ASP - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - LEU Joining LEU - HIE Joining HIE - TYR Joining TYR - THR Joining THR - ASP Joining ASP - TRP Joining TRP - LEU Joining LEU - HIE Joining HIE - PRO Joining PRO - GLU Joining GLU - ASP Joining ASP - PRO Joining PRO - THR Joining THR - HIE Joining HIE - LEU Joining LEU - ARG Joining ARG - ASP Joining ASP - ALA Joining ALA - MET Joining MET - SER Joining SER - ALA Joining ALA - VAL Joining VAL - VAL Joining VAL - GLY Joining GLY - ASP Joining ASP - HIE Joining HIE - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - CYX Joining CYX - PRO Joining PRO - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - LEU Joining LEU - ALA Joining ALA - GLY Joining GLY - ARG Joining ARG - LEU Joining LEU - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - ARG Joining ARG - VAL Joining VAL - TYR Joining TYR - ALA Joining ALA - TYR Joining TYR - ILE Joining ILE - PHE Joining PHE - GLU Joining GLU - HIE Joining HIE - ARG Joining ARG - ALA Joining ALA - SER Joining SER - THR Joining THR - LEU Joining LEU - THR Joining THR - TRP Joining TRP - PRO Joining PRO - LEU Joining LEU - TRP Joining TRP - MET Joining MET - GLY Joining GLY - VAL Joining VAL - PRO Joining PRO - HIE Joining HIE - GLY Joining GLY - TYR Joining TYR - GLU Joining GLU - ILE Joining ILE - GLU Joining GLU - PHE Joining PHE - ILE Joining ILE - PHE Joining PHE - GLY Joining GLY - LEU Joining LEU - PRO Joining PRO - LEU Joining LEU - ASP Joining ASP - PRO Joining PRO - SER Joining SER - LEU Joining LEU - ASN Joining ASN - TYR Joining TYR - THR Joining THR - THR Joining THR - GLU Joining GLU - GLU Joining GLU - ARG Joining ARG - ILE Joining ILE - PHE Joining PHE - ALA Joining ALA - GLN Joining GLN - ARG Joining ARG - LEU Joining LEU - MET Joining MET - LYS Joining LYS - TYR Joining TYR - TRP Joining TRP - THR Joining THR - ASN Joining ASN - PHE Joining PHE - ALA Joining ALA - ARG Joining ARG - THR Joining THR - GLY Joining GLY - ASP Joining ASP - PRO Joining PRO - ASN Joining ASN - ASP Joining ASP - PRO Joining PRO - ARG Joining ARG - ASP Joining ASP - SER Joining SER - LYS Joining LYS - SER Joining SER - PRO Joining PRO - GLN Joining GLN - TRP Joining TRP - PRO Joining PRO - PRO Joining PRO - TYR Joining TYR - THR Joining THR - THR Joining THR - ALA Joining ALA - ALA Joining ALA - GLN Joining GLN - GLN Joining GLN - TYR Joining TYR - VAL Joining VAL - SER Joining SER - LEU Joining LEU - ASN Joining ASN - LEU Joining LEU - LYS Joining LYS - PRO Joining PRO - LEU Joining LEU - GLU Joining GLU - VAL Joining VAL - ARG Joining ARG - ARG Joining ARG - GLY Joining GLY - LEU Joining LEU - ARG Joining ARG - ALA Joining ALA - GLN Joining GLN - THR Joining THR - CYX Joining CYX - ALA Joining ALA - PHE Joining PHE - TRP Joining TRP - ASN Joining ASN - ARG Joining ARG - PHE Joining PHE - LEU Joining LEU - PRO Joining PRO - LYS Joining LYS - LEU Joining LEU - LEU Joining LEU - SER Joining SER - ALA Joining ALA - CTHR Added missing heavy atom: .R.A total atoms in file: 4231 Leap added 4126 missing atoms according to residue templates: 1 Heavy 4125 H / lone pairs > bond p.69.SG p.96.SG > bond p.257.SG p.272.SG > bond p.409.SG p.529.SG > check p Checking 'p'.... WARNING: The unperturbed charge of the unit: -9.000000 is not zero. Warning: Close contact of 1.436988 angstroms between .R.A and .R.A Warning: Close contact of 1.064744 angstroms between .R.A and .R.A Warning: Close contact of 1.488587 angstroms between .R.A and .R.A Warning: Close contact of 0.465251 angstroms between .R.A and .R.A Warning: Close contact of 1.365519 angstroms between .R.A and .R.A Warning: Close contact of 0.996688 angstroms between .R.A and .R.A Warning: Close contact of 0.804671 angstroms between .R.A and .R.A Checking parameters for unit 'p'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 8 Unit is OK. > saveamberparm p protein.prmtop protein.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -9.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. ** No torsion terms for CT-NT-P-OS ** No torsion terms for CT-NT-P-OS ** No torsion terms for OS-P-NT-CT ** No torsion terms for OS-P-NT-CT Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1772 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Parameter file was not saved. > quit Quit