log started: Mon Jul 21 10:26:01 2008 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /data/deb/amber9/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /data/deb/amber9/dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /data/deb/amber9/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: /data/deb/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /data/deb/amber9/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. >> # >> loadOff all_aminoct94.lib Loading library: /data/deb/amber9/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: /data/deb/amber9/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 >> loadOff all_amino03.lib Loading library: /data/deb/amber9/dat/leap/lib/all_amino03.lib Loading: ACE 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > # load the parameter set for metals > mtl = loadamberparams /data/sandy/Desktop/3/Required_parms/metals.dat Loading parameters: /data/sandy/Desktop/3/Required_parms/metals.dat Reading force field modification type file (frcmod) Reading title: Ca2+ and Mn2+ vdw parameters from Concanavalin A study (UNKNOWN ATOM TYPE: MN) (UNKNOWN ATOM TYPE: KA) > # load the preparatory files for Metals viz. Mn2+ and Ca2+ > loadamberprep /data/sandy/Desktop/3/Required_parms/metals.prp Loading Prep file: /data/sandy/Desktop/3/Required_parms/metals.prp (UNKNOWN ATOM TYPE: KA) (UNKNOWN ATOM TYPE: MN) Loaded UNIT: CAL Loaded UNIT: MNG > loadoff /data/sandy/Desktop/3/Required_parms/pos4.lib Loading library: /data/sandy/Desktop/3/Required_parms/pos4.lib Loading: pos > HOH = TP3 > WAT = TP3 > # > # > # assumes most users want to use tip3p as the explicit solvent model > # but this can easily switched by the following commands in leap: > # WAT = TP5 > # loadamberparams frcmod.tip5p > # > ec=loadpdb e2is.pdb Loading PDB file: ./e2is.pdb Enter zPdbReadScan from call depth 0. -- residue 258: duplicate [ CB] atoms (total 2) -- residue 258: duplicate [ OG] atoms (total 2) -- residue 3: duplicate [ CB] atoms (total 2) -- residue 3: duplicate [ CG2] atoms (total 2) -- residue 3: duplicate [ OG1] atoms (total 2) -- residue 264: duplicate [ C] atoms (total 2) -- residue 264: duplicate [ CA] atoms (total 2) -- residue 264: duplicate [ CB] atoms (total 2) -- residue 264: duplicate [ CG] atoms (total 2) -- residue 264: duplicate [ N] atoms (total 2) -- residue 264: duplicate [ ND2] atoms (total 2) -- residue 264: duplicate [ O] atoms (total 2) -- residue 264: duplicate [ OD1] atoms (total 2) -- residue 9: duplicate [ CB] atoms (total 2) -- residue 9: duplicate [ OG] atoms (total 2) -- residue 269: duplicate [ CB] atoms (total 2) -- residue 269: duplicate [ CD1] atoms (total 2) -- residue 269: duplicate [ CD2] atoms (total 2) -- residue 269: duplicate [ CG] atoms (total 2) -- residue 15: duplicate [ C] atoms (total 2) -- residue 15: duplicate [ CA] atoms (total 2) -- residue 15: duplicate [ CB] atoms (total 2) -- residue 15: duplicate [ CG] atoms (total 2) -- residue 15: duplicate [ N] atoms (total 2) -- residue 15: duplicate [ ND2] atoms (total 2) -- residue 15: duplicate [ O] atoms (total 2) -- residue 15: duplicate [ OD1] atoms (total 2) -- residue 20: duplicate [ CB] atoms (total 2) -- residue 20: duplicate [ CD1] atoms (total 2) -- residue 20: duplicate [ CD2] atoms (total 2) -- residue 20: duplicate [ CG] atoms (total 2) -- residue 301: duplicate [ CB] atoms (total 2) -- residue 301: duplicate [ CD1] atoms (total 2) -- residue 301: duplicate [ CD2] atoms (total 2) -- residue 301: duplicate [ CG] atoms (total 2) -- residue 306: duplicate [ CB] atoms (total 2) -- residue 306: duplicate [ CG1] atoms (total 2) -- residue 306: duplicate [ CG2] atoms (total 2) -- residue 52: duplicate [ CB] atoms (total 2) -- residue 52: duplicate [ CD1] atoms (total 2) -- residue 52: duplicate [ CD2] atoms (total 2) -- residue 52: duplicate [ CG] atoms (total 2) -- residue 57: duplicate [ CB] atoms (total 2) -- residue 57: duplicate [ CG1] atoms (total 2) -- residue 57: duplicate [ CG2] atoms (total 2) -- residue 324: duplicate [ CB] atoms (total 2) -- residue 324: duplicate [ OG] atoms (total 2) -- residue 75: duplicate [ CB] atoms (total 2) -- residue 75: duplicate [ OG] atoms (total 2) -- residue 373: duplicate [ CB] atoms (total 2) -- residue 373: duplicate [ CD1] atoms (total 2) -- residue 373: duplicate [ CD2] atoms (total 2) -- residue 373: duplicate [ CG] atoms (total 2) -- residue 124: duplicate [ CB] atoms (total 2) -- residue 124: duplicate [ CD1] atoms (total 2) -- residue 124: duplicate [ CD2] atoms (total 2) -- residue 124: duplicate [ CG] atoms (total 2) -- residue 424: duplicate [ CB] atoms (total 2) -- residue 424: duplicate [ OG] atoms (total 2) -- residue 428: duplicate [ CB] atoms (total 2) -- residue 428: duplicate [ CD1] atoms (total 2) -- residue 428: duplicate [ CD2] atoms (total 2) -- residue 428: duplicate [ CG] atoms (total 2) -- residue 175: duplicate [ CB] atoms (total 2) -- residue 175: duplicate [ OG] atoms (total 2) -- residue 432: duplicate [ CB] atoms (total 2) -- residue 432: duplicate [ CD1] atoms (total 2) -- residue 432: duplicate [ CD2] atoms (total 2) -- residue 432: duplicate [ CG] atoms (total 2) -- residue 179: duplicate [ CB] atoms (total 2) -- residue 179: duplicate [ CD1] atoms (total 2) -- residue 179: duplicate [ CD2] atoms (total 2) -- residue 179: duplicate [ CG] atoms (total 2) -- residue 183: duplicate [ CB] atoms (total 2) -- residue 183: duplicate [ CD1] atoms (total 2) -- residue 183: duplicate [ CD2] atoms (total 2) -- residue 183: duplicate [ CG] atoms (total 2) -- residue 442: duplicate [ CB] atoms (total 2) -- residue 442: duplicate [ CG2] atoms (total 2) -- residue 442: duplicate [ OG1] atoms (total 2) -- residue 193: duplicate [ CB] atoms (total 2) -- residue 193: duplicate [ CG2] atoms (total 2) -- residue 193: duplicate [ OG1] atoms (total 2) -- residue 252: duplicate [ CB] atoms (total 2) -- residue 252: duplicate [ CG2] atoms (total 2) -- residue 252: duplicate [ OG1] atoms (total 2) ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE: (same-name atoms are reduced to a single atom) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue VAL, term: Terminal/beginning, seq. number: 0 to: NVAL. (Residue 1: GLU, Nonterminal, was not found in name map.) (Residue 2: THR, Nonterminal, was not found in name map.) (Residue 3: ILE, Nonterminal, was not found in name map.) (Residue 4: SER, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: SER, Nonterminal, was not found in name map.) (Residue 7: PHE, Nonterminal, was not found in name map.) (Residue 8: SER, Nonterminal, was not found in name map.) (Residue 9: GLU, Nonterminal, was not found in name map.) (Residue 10: PHE, Nonterminal, was not found in name map.) (Residue 11: GLU, Nonterminal, was not found in name map.) (Residue 12: PRO, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASN, Nonterminal, was not found in name map.) (Residue 15: ASP, Nonterminal, was not found in name map.) (Residue 16: ASN, Nonterminal, was not found in name map.) (Residue 17: LEU, Nonterminal, was not found in name map.) (Residue 18: THR, Nonterminal, was not found in name map.) (Residue 19: LEU, Nonterminal, was not found in name map.) (Residue 20: GLN, Nonterminal, was not found in name map.) (Residue 21: GLY, Nonterminal, was not found in name map.) (Residue 22: ALA, Nonterminal, was not found in name map.) (Residue 23: ALA, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: ILE, Nonterminal, was not found in name map.) (Residue 26: THR, Nonterminal, was not found in name map.) (Residue 27: GLN, 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: VAL, Nonterminal, was not found in name map.) (Residue 31: LEU, Nonterminal, was not found in name map.) (Residue 32: GLN, Nonterminal, was not found in name map.) (Residue 33: LEU, Nonterminal, was not found in name map.) (Residue 34: THR, Nonterminal, was not found in name map.) (Residue 35: LYS, Nonterminal, was not found in name map.) (Residue 36: ILE, Nonterminal, was not found in name map.) (Residue 37: ASN, Nonterminal, was not found in name map.) (Residue 38: GLN, Nonterminal, was not found in name map.) (Residue 39: ASN, Nonterminal, was not found in name map.) (Residue 40: GLY, Nonterminal, was not found in name map.) (Residue 41: MET, Nonterminal, was not found in name map.) (Residue 42: PRO, Nonterminal, was not found in name map.) (Residue 43: ALA, Nonterminal, was not found in name map.) (Residue 44: TRP, Nonterminal, was not found in name map.) (Residue 45: ASP, Nonterminal, was not found in name map.) (Residue 46: SER, Nonterminal, was not found in name map.) (Residue 47: THR, Nonterminal, was not found in name map.) (Residue 48: GLY, Nonterminal, was not found in name map.) (Residue 49: ARG, Nonterminal, was not found in name map.) (Residue 50: THR, Nonterminal, was not found in name map.) (Residue 51: LEU, Nonterminal, was not found in name map.) (Residue 52: TYR, Nonterminal, was not found in name map.) (Residue 53: ALA, Nonterminal, was not found in name map.) (Residue 54: LYS, Nonterminal, was not found in name map.) (Residue 55: PRO, Nonterminal, was not found in name map.) (Residue 56: VAL, Nonterminal, was not found in name map.) (Residue 57: HIS, Nonterminal, was not found in name map.) (Residue 58: ILE, Nonterminal, was not found in name map.) (Residue 59: TRP, Nonterminal, was not found in name map.) (Residue 60: ASP, Nonterminal, was not found in name map.) (Residue 61: MET, 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: GLY, Nonterminal, was not found in name map.) (Residue 65: THR, Nonterminal, was not found in name map.) (Residue 66: VAL, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: SER, Nonterminal, was not found in name map.) (Residue 69: PHE, Nonterminal, was not found in name map.) (Residue 70: GLU, Nonterminal, was not found in name map.) (Residue 71: THR, Nonterminal, was not found in name map.) (Residue 72: ARG, Nonterminal, was not found in name map.) (Residue 73: PHE, Nonterminal, was not found in name map.) (Residue 74: SER, Nonterminal, was not found in name map.) (Residue 75: PHE, Nonterminal, was not found in name map.) (Residue 76: SER, Nonterminal, was not found in name map.) (Residue 77: ILE, Nonterminal, was not found in name map.) (Residue 78: GLU, Nonterminal, was not found in name map.) (Residue 79: GLN, Nonterminal, was not found in name map.) (Residue 80: PRO, Nonterminal, was not found in name map.) (Residue 81: TYR, Nonterminal, was not found in name map.) (Residue 82: THR, Nonterminal, was not found in name map.) (Residue 83: ARG, Nonterminal, was not found in name map.) (Residue 84: PRO, Nonterminal, was not found in name map.) (Residue 85: LEU, Nonterminal, was not found in name map.) (Residue 86: PRO, Nonterminal, was not found in name map.) (Residue 87: ALA, Nonterminal, was not found in name map.) (Residue 88: ASP, Nonterminal, was not found in name map.) (Residue 89: GLY, Nonterminal, was not found in name map.) (Residue 90: LEU, Nonterminal, was not found in name map.) (Residue 91: VAL, Nonterminal, was not found in name map.) (Residue 92: PHE, Nonterminal, was not found in name map.) (Residue 93: PHE, Nonterminal, was not found in name map.) (Residue 94: MET, Nonterminal, was not found in name map.) (Residue 95: GLY, Nonterminal, was not found in name map.) (Residue 96: PRO, Nonterminal, was not found in name map.) (Residue 97: THR, Nonterminal, was not found in name map.) (Residue 98: LYS, Nonterminal, was not found in name map.) (Residue 99: SER, Nonterminal, was not found in name map.) (Residue 100: LYS, Nonterminal, was not found in name map.) (Residue 101: PRO, Nonterminal, was not found in name map.) (Residue 102: ALA, Nonterminal, was not found in name map.) (Residue 103: GLN, Nonterminal, was not found in name map.) (Residue 104: GLY, Nonterminal, was not found in name map.) (Residue 105: TYR, Nonterminal, was not found in name map.) (Residue 106: GLY, Nonterminal, was not found in name map.) (Residue 107: TYR, Nonterminal, was not found in name map.) (Residue 108: LEU, Nonterminal, was not found in name map.) (Residue 109: GLY, Nonterminal, was not found in name map.) (Residue 110: ILE, Nonterminal, was not found in name map.) (Residue 111: PHE, Nonterminal, was not found in name map.) (Residue 112: ASN, Nonterminal, was not found in name map.) (Residue 113: ASN, Nonterminal, was not found in name map.) (Residue 114: SER, Nonterminal, was not found in name map.) (Residue 115: LYS, Nonterminal, was not found in name map.) (Residue 116: GLN, Nonterminal, was not found in name map.) (Residue 117: ASP, Nonterminal, was not found in name map.) (Residue 118: ASN, Nonterminal, was not found in name map.) (Residue 119: SER, Nonterminal, was not found in name map.) (Residue 120: TYR, Nonterminal, was not found in name map.) (Residue 121: GLN, Nonterminal, was not found in name map.) (Residue 122: THR, Nonterminal, was not found in name map.) (Residue 123: LEU, Nonterminal, was not found in name map.) (Residue 124: GLY, Nonterminal, was not found in name map.) (Residue 125: VAL, Nonterminal, was not found in name map.) (Residue 126: GLU, Nonterminal, was not found in name map.) (Residue 127: PHE, Nonterminal, was not found in name map.) (Residue 128: ASP, Nonterminal, was not found in name map.) (Residue 129: THR, Nonterminal, was not found in name map.) (Residue 130: PHE, Nonterminal, was not found in name map.) (Residue 131: SER, Nonterminal, was not found in name map.) (Residue 132: ASN, Nonterminal, was not found in name map.) (Residue 133: PRO, Nonterminal, was not found in name map.) (Residue 134: TRP, Nonterminal, was not found in name map.) (Residue 135: ASP, Nonterminal, was not found in name map.) (Residue 136: PRO, Nonterminal, was not found in name map.) (Residue 137: PRO, Nonterminal, was not found in name map.) (Residue 138: GLN, Nonterminal, was not found in name map.) (Residue 139: VAL, Nonterminal, was not found in name map.) (Residue 140: PRO, Nonterminal, was not found in name map.) (Residue 141: HIS, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: GLY, Nonterminal, was not found in name map.) (Residue 144: ILE, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: VAL, Nonterminal, was not found in name map.) (Residue 147: ASN, Nonterminal, was not found in name map.) (Residue 148: SER, Nonterminal, was not found in name map.) (Residue 149: ILE, Nonterminal, was not found in name map.) (Residue 150: ARG, Nonterminal, was not found in name map.) (Residue 151: SER, Nonterminal, was not found in name map.) (Residue 152: ILE, Nonterminal, was not found in name map.) (Residue 153: LYS, Nonterminal, was not found in name map.) (Residue 154: THR, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: PRO, Nonterminal, was not found in name map.) (Residue 157: PHE, Nonterminal, was not found in name map.) (Residue 158: GLN, Nonterminal, was not found in name map.) (Residue 159: LEU, Nonterminal, was not found in name map.) (Residue 160: ASP, Nonterminal, was not found in name map.) (Residue 161: ASN, Nonterminal, was not found in name map.) (Residue 162: GLY, Nonterminal, was not found in name map.) (Residue 163: GLN, Nonterminal, was not found in name map.) (Residue 164: VAL, Nonterminal, was not found in name map.) (Residue 165: ALA, Nonterminal, was not found in name map.) (Residue 166: ASN, Nonterminal, was not found in name map.) (Residue 167: VAL, Nonterminal, was not found in name map.) (Residue 168: VAL, Nonterminal, was not found in name map.) (Residue 169: ILE, Nonterminal, was not found in name map.) (Residue 170: LYS, Nonterminal, was not found in name map.) (Residue 171: TYR, Nonterminal, was not found in name map.) (Residue 172: ASP, Nonterminal, was not found in name map.) (Residue 173: ALA, Nonterminal, was not found in name map.) (Residue 174: SER, Nonterminal, was not found in name map.) (Residue 175: SER, Nonterminal, was not found in name map.) (Residue 176: LYS, Nonterminal, was not found in name map.) (Residue 177: ILE, Nonterminal, was not found in name map.) (Residue 178: LEU, Nonterminal, was not found in name map.) (Residue 179: HIS, Nonterminal, was not found in name map.) (Residue 180: ALA, Nonterminal, was not found in name map.) (Residue 181: VAL, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: VAL, Nonterminal, was not found in name map.) (Residue 184: TYR, Nonterminal, was not found in name map.) (Residue 185: PRO, Nonterminal, was not found in name map.) (Residue 186: SER, Nonterminal, was not found in name map.) (Residue 187: SER, Nonterminal, was not found in name map.) (Residue 188: GLY, Nonterminal, was not found in name map.) (Residue 189: ALA, Nonterminal, was not found in name map.) (Residue 190: ILE, Nonterminal, was not found in name map.) (Residue 191: TYR, Nonterminal, was not found in name map.) (Residue 192: THR, Nonterminal, was not found in name map.) (Residue 193: ILE, Nonterminal, was not found in name map.) (Residue 194: ALA, Nonterminal, was not found in name map.) (Residue 195: GLU, Nonterminal, was not found in name map.) (Residue 196: ILE, Nonterminal, was not found in name map.) (Residue 197: VAL, Nonterminal, was not found in name map.) (Residue 198: ASP, Nonterminal, was not found in name map.) (Residue 199: VAL, Nonterminal, was not found in name map.) (Residue 200: LYS, Nonterminal, was not found in name map.) (Residue 201: GLN, Nonterminal, was not found in name map.) (Residue 202: VAL, Nonterminal, was not found in name map.) (Residue 203: LEU, Nonterminal, was not found in name map.) (Residue 204: PRO, Nonterminal, was not found in name map.) (Residue 205: GLU, Nonterminal, was not found in name map.) (Residue 206: TRP, Nonterminal, was not found in name map.) (Residue 207: VAL, Nonterminal, was not found in name map.) (Residue 208: ASP, Nonterminal, was not found in name map.) (Residue 209: VAL, Nonterminal, was not found in name map.) (Residue 210: GLY, Nonterminal, was not found in name map.) (Residue 211: LEU, Nonterminal, was not found in name map.) (Residue 212: SER, Nonterminal, was not found in name map.) (Residue 213: GLY, Nonterminal, was not found in name map.) (Residue 214: ALA, Nonterminal, was not found in name map.) (Residue 215: THR, Nonterminal, was not found in name map.) (Residue 216: GLY, Nonterminal, was not found in name map.) (Residue 217: ALA, Nonterminal, was not found in name map.) (Residue 218: GLN, Nonterminal, was not found in name map.) (Residue 219: ARG, Nonterminal, was not found in name map.) (Residue 220: ASP, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: ALA, Nonterminal, was not found in name map.) (Residue 223: GLU, Nonterminal, was not found in name map.) (Residue 224: THR, Nonterminal, was not found in name map.) (Residue 225: HIS, Nonterminal, was not found in name map.) (Residue 226: ASP, Nonterminal, was not found in name map.) (Residue 227: VAL, Nonterminal, was not found in name map.) (Residue 228: TYR, Nonterminal, was not found in name map.) (Residue 229: SER, Nonterminal, was not found in name map.) (Residue 230: TRP, Nonterminal, was not found in name map.) (Residue 231: SER, Nonterminal, was not found in name map.) (Residue 232: PHE, Nonterminal, was not found in name map.) (Residue 233: GLN, Nonterminal, was not found in name map.) (Residue 234: ALA, Nonterminal, was not found in name map.) (Residue 235: SER, Nonterminal, was not found in name map.) (Residue 236: LEU, Nonterminal, was not found in name map.) (Residue 237: PRO, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 238 to: CGLU. (Residue 239: MNG, Terminal/last, was not found in name map.) (Residue 240: CAL, Terminal/last, was not found in name map.) (Residue 241: WYB, Terminal/last, was not found in name map.) (Residue 242: 0fA, Terminal/last, was not found in name map.) (Residue 243: 4YB, Terminal/last, was not found in name map.) (Residue 244: SMB, Terminal/last, was not found in name map.) (Residue 245: 0XB, Terminal/last, was not found in name map.) (Residue 246: 0MA, Terminal/last, was not found in name map.) (Residue 247: 0MA, Terminal/last, was not found in name map.) (Residue 248: 1VA, Terminal/last, was not found in name map.) Mapped residue VAL, term: Terminal/beginning, seq. number: 249 to: NVAL. (Residue 250: GLU, Nonterminal, was not found in name map.) (Residue 251: THR, Nonterminal, was not found in name map.) (Residue 252: ILE, Nonterminal, was not found in name map.) (Residue 253: SER, Nonterminal, was not found in name map.) (Residue 254: PHE, Nonterminal, was not found in name map.) (Residue 255: SER, Nonterminal, was not found in name map.) (Residue 256: PHE, Nonterminal, was not found in name map.) (Residue 257: SER, Nonterminal, was not found in name map.) (Residue 258: GLU, Nonterminal, was not found in name map.) (Residue 259: PHE, Nonterminal, was not found in name map.) (Residue 260: GLU, Nonterminal, was not found in name map.) (Residue 261: PRO, Nonterminal, was not found in name map.) (Residue 262: GLY, Nonterminal, was not found in name map.) (Residue 263: ASN, Nonterminal, was not found in name map.) (Residue 264: ASP, Nonterminal, was not found in name map.) (Residue 265: ASN, Nonterminal, was not found in name map.) (Residue 266: LEU, Nonterminal, was not found in name map.) (Residue 267: THR, Nonterminal, was not found in name map.) (Residue 268: LEU, Nonterminal, was not found in name map.) (Residue 269: GLN, Nonterminal, was not found in name map.) (Residue 270: GLY, Nonterminal, was not found in name map.) (Residue 271: ALA, Nonterminal, was not found in name map.) (Residue 272: ALA, Nonterminal, was not found in name map.) (Residue 273: LEU, Nonterminal, was not found in name map.) (Residue 274: ILE, Nonterminal, was not found in name map.) (Residue 275: THR, Nonterminal, was not found in name map.) (Residue 276: GLN, Nonterminal, was not found in name map.) (Residue 277: SER, Nonterminal, was not found in name map.) (Residue 278: GLY, Nonterminal, was not found in name map.) (Residue 279: VAL, Nonterminal, was not found in name map.) (Residue 280: LEU, Nonterminal, was not found in name map.) (Residue 281: GLN, Nonterminal, was not found in name map.) (Residue 282: LEU, Nonterminal, was not found in name map.) (Residue 283: THR, Nonterminal, was not found in name map.) (Residue 284: LYS, Nonterminal, was not found in name map.) (Residue 285: ILE, Nonterminal, was not found in name map.) (Residue 286: ASN, Nonterminal, was not found in name map.) (Residue 287: GLN, Nonterminal, was not found in name map.) (Residue 288: ASN, Nonterminal, was not found in name map.) (Residue 289: GLY, Nonterminal, was not found in name map.) (Residue 290: MET, Nonterminal, was not found in name map.) (Residue 291: PRO, Nonterminal, was not found in name map.) (Residue 292: ALA, Nonterminal, was not found in name map.) (Residue 293: TRP, Nonterminal, was not found in name map.) (Residue 294: ASP, Nonterminal, was not found in name map.) (Residue 295: SER, Nonterminal, was not found in name map.) (Residue 296: THR, Nonterminal, was not found in name map.) (Residue 297: GLY, Nonterminal, was not found in name map.) (Residue 298: ARG, Nonterminal, was not found in name map.) (Residue 299: THR, Nonterminal, was not found in name map.) (Residue 300: LEU, Nonterminal, was not found in name map.) (Residue 301: TYR, Nonterminal, was not found in name map.) (Residue 302: ALA, Nonterminal, was not found in name map.) (Residue 303: LYS, Nonterminal, was not found in name map.) (Residue 304: PRO, Nonterminal, was not found in name map.) (Residue 305: VAL, Nonterminal, was not found in name map.) (Residue 306: HIS, Nonterminal, was not found in name map.) (Residue 307: ILE, Nonterminal, was not found in name map.) (Residue 308: TRP, Nonterminal, was not found in name map.) (Residue 309: ASP, Nonterminal, was not found in name map.) (Residue 310: MET, Nonterminal, was not found in name map.) (Residue 311: THR, Nonterminal, was not found in name map.) (Residue 312: THR, Nonterminal, was not found in name map.) (Residue 313: GLY, Nonterminal, was not found in name map.) (Residue 314: THR, Nonterminal, was not found in name map.) (Residue 315: VAL, Nonterminal, was not found in name map.) (Residue 316: ALA, Nonterminal, was not found in name map.) (Residue 317: SER, Nonterminal, was not found in name map.) (Residue 318: PHE, Nonterminal, was not found in name map.) (Residue 319: GLU, Nonterminal, was not found in name map.) (Residue 320: THR, Nonterminal, was not found in name map.) (Residue 321: ARG, Nonterminal, was not found in name map.) (Residue 322: PHE, Nonterminal, was not found in name map.) (Residue 323: SER, Nonterminal, was not found in name map.) (Residue 324: PHE, Nonterminal, was not found in name map.) (Residue 325: SER, Nonterminal, was not found in name map.) (Residue 326: ILE, Nonterminal, was not found in name map.) (Residue 327: GLU, Nonterminal, was not found in name map.) (Residue 328: GLN, Nonterminal, was not found in name map.) (Residue 329: PRO, Nonterminal, was not found in name map.) (Residue 330: TYR, Nonterminal, was not found in name map.) (Residue 331: THR, Nonterminal, was not found in name map.) (Residue 332: ARG, Nonterminal, was not found in name map.) (Residue 333: PRO, Nonterminal, was not found in name map.) (Residue 334: LEU, Nonterminal, was not found in name map.) (Residue 335: PRO, Nonterminal, was not found in name map.) (Residue 336: ALA, Nonterminal, was not found in name map.) (Residue 337: ASP, Nonterminal, was not found in name map.) (Residue 338: GLY, Nonterminal, was not found in name map.) (Residue 339: LEU, Nonterminal, was not found in name map.) (Residue 340: VAL, Nonterminal, was not found in name map.) (Residue 341: PHE, Nonterminal, was not found in name map.) (Residue 342: PHE, Nonterminal, was not found in name map.) (Residue 343: MET, Nonterminal, was not found in name map.) (Residue 344: GLY, Nonterminal, was not found in name map.) (Residue 345: PRO, Nonterminal, was not found in name map.) (Residue 346: THR, Nonterminal, was not found in name map.) (Residue 347: LYS, Nonterminal, was not found in name map.) (Residue 348: SER, Nonterminal, was not found in name map.) (Residue 349: LYS, Nonterminal, was not found in name map.) (Residue 350: PRO, Nonterminal, was not found in name map.) (Residue 351: ALA, Nonterminal, was not found in name map.) (Residue 352: GLN, Nonterminal, was not found in name map.) (Residue 353: GLY, Nonterminal, was not found in name map.) (Residue 354: TYR, Nonterminal, was not found in name map.) (Residue 355: GLY, Nonterminal, was not found in name map.) (Residue 356: TYR, Nonterminal, was not found in name map.) (Residue 357: LEU, Nonterminal, was not found in name map.) (Residue 358: GLY, Nonterminal, was not found in name map.) (Residue 359: ILE, Nonterminal, was not found in name map.) (Residue 360: PHE, Nonterminal, was not found in name map.) (Residue 361: ASN, Nonterminal, was not found in name map.) (Residue 362: ASN, Nonterminal, was not found in name map.) (Residue 363: SER, Nonterminal, was not found in name map.) (Residue 364: LYS, Nonterminal, was not found in name map.) (Residue 365: GLN, Nonterminal, was not found in name map.) (Residue 366: ASP, Nonterminal, was not found in name map.) (Residue 367: ASN, Nonterminal, was not found in name map.) (Residue 368: SER, Nonterminal, was not found in name map.) (Residue 369: TYR, Nonterminal, was not found in name map.) (Residue 370: GLN, Nonterminal, was not found in name map.) (Residue 371: THR, Nonterminal, was not found in name map.) (Residue 372: LEU, Nonterminal, was not found in name map.) (Residue 373: GLY, Nonterminal, was not found in name map.) (Residue 374: VAL, Nonterminal, was not found in name map.) (Residue 375: GLU, Nonterminal, was not found in name map.) (Residue 376: PHE, Nonterminal, was not found in name map.) (Residue 377: ASP, Nonterminal, was not found in name map.) (Residue 378: THR, Nonterminal, was not found in name map.) (Residue 379: PHE, Nonterminal, was not found in name map.) (Residue 380: SER, Nonterminal, was not found in name map.) (Residue 381: ASN, Nonterminal, was not found in name map.) (Residue 382: PRO, Nonterminal, was not found in name map.) (Residue 383: TRP, Nonterminal, was not found in name map.) (Residue 384: ASP, Nonterminal, was not found in name map.) (Residue 385: PRO, Nonterminal, was not found in name map.) (Residue 386: PRO, Nonterminal, was not found in name map.) (Residue 387: GLN, Nonterminal, was not found in name map.) (Residue 388: VAL, Nonterminal, was not found in name map.) (Residue 389: PRO, Nonterminal, was not found in name map.) (Residue 390: HIS, Nonterminal, was not found in name map.) (Residue 391: ILE, Nonterminal, was not found in name map.) (Residue 392: GLY, Nonterminal, was not found in name map.) (Residue 393: ILE, Nonterminal, was not found in name map.) (Residue 394: ASP, Nonterminal, was not found in name map.) (Residue 395: VAL, Nonterminal, was not found in name map.) (Residue 396: ASN, Nonterminal, was not found in name map.) (Residue 397: SER, Nonterminal, was not found in name map.) (Residue 398: ILE, Nonterminal, was not found in name map.) (Residue 399: ARG, Nonterminal, was not found in name map.) (Residue 400: SER, Nonterminal, was not found in name map.) (Residue 401: ILE, Nonterminal, was not found in name map.) (Residue 402: LYS, Nonterminal, was not found in name map.) (Residue 403: THR, Nonterminal, was not found in name map.) (Residue 404: GLN, Nonterminal, was not found in name map.) (Residue 405: PRO, Nonterminal, was not found in name map.) (Residue 406: PHE, Nonterminal, was not found in name map.) (Residue 407: GLN, Nonterminal, was not found in name map.) (Residue 408: LEU, Nonterminal, was not found in name map.) (Residue 409: ASP, Nonterminal, was not found in name map.) (Residue 410: ASN, Nonterminal, was not found in name map.) (Residue 411: GLY, Nonterminal, was not found in name map.) (Residue 412: GLN, Nonterminal, was not found in name map.) (Residue 413: VAL, Nonterminal, was not found in name map.) (Residue 414: ALA, Nonterminal, was not found in name map.) (Residue 415: ASN, Nonterminal, was not found in name map.) (Residue 416: VAL, Nonterminal, was not found in name map.) (Residue 417: VAL, Nonterminal, was not found in name map.) (Residue 418: ILE, Nonterminal, was not found in name map.) (Residue 419: LYS, Nonterminal, was not found in name map.) (Residue 420: TYR, Nonterminal, was not found in name map.) (Residue 421: ASP, Nonterminal, was not found in name map.) (Residue 422: ALA, Nonterminal, was not found in name map.) (Residue 423: SER, Nonterminal, was not found in name map.) (Residue 424: SER, Nonterminal, was not found in name map.) (Residue 425: LYS, Nonterminal, was not found in name map.) (Residue 426: ILE, Nonterminal, was not found in name map.) (Residue 427: LEU, Nonterminal, was not found in name map.) (Residue 428: HIS, Nonterminal, was not found in name map.) (Residue 429: ALA, Nonterminal, was not found in name map.) (Residue 430: VAL, Nonterminal, was not found in name map.) (Residue 431: LEU, Nonterminal, was not found in name map.) (Residue 432: VAL, Nonterminal, was not found in name map.) (Residue 433: TYR, Nonterminal, was not found in name map.) (Residue 434: PRO, Nonterminal, was not found in name map.) (Residue 435: SER, Nonterminal, was not found in name map.) (Residue 436: SER, Nonterminal, was not found in name map.) (Residue 437: GLY, Nonterminal, was not found in name map.) (Residue 438: ALA, Nonterminal, was not found in name map.) (Residue 439: ILE, Nonterminal, was not found in name map.) (Residue 440: TYR, Nonterminal, was not found in name map.) (Residue 441: THR, Nonterminal, was not found in name map.) (Residue 442: ILE, Nonterminal, was not found in name map.) (Residue 443: ALA, Nonterminal, was not found in name map.) (Residue 444: GLU, Nonterminal, was not found in name map.) (Residue 445: ILE, Nonterminal, was not found in name map.) (Residue 446: VAL, Nonterminal, was not found in name map.) (Residue 447: ASP, Nonterminal, was not found in name map.) (Residue 448: VAL, Nonterminal, was not found in name map.) (Residue 449: LYS, Nonterminal, was not found in name map.) (Residue 450: GLN, Nonterminal, was not found in name map.) (Residue 451: VAL, Nonterminal, was not found in name map.) (Residue 452: LEU, Nonterminal, was not found in name map.) (Residue 453: PRO, Nonterminal, was not found in name map.) (Residue 454: GLU, Nonterminal, was not found in name map.) (Residue 455: TRP, Nonterminal, was not found in name map.) (Residue 456: VAL, Nonterminal, was not found in name map.) (Residue 457: ASP, Nonterminal, was not found in name map.) (Residue 458: VAL, Nonterminal, was not found in name map.) (Residue 459: GLY, Nonterminal, was not found in name map.) (Residue 460: LEU, Nonterminal, was not found in name map.) (Residue 461: SER, Nonterminal, was not found in name map.) (Residue 462: GLY, Nonterminal, was not found in name map.) (Residue 463: ALA, Nonterminal, was not found in name map.) (Residue 464: THR, Nonterminal, was not found in name map.) (Residue 465: GLY, Nonterminal, was not found in name map.) (Residue 466: ALA, Nonterminal, was not found in name map.) (Residue 467: GLN, Nonterminal, was not found in name map.) (Residue 468: ARG, Nonterminal, was not found in name map.) (Residue 469: ASP, Nonterminal, was not found in name map.) (Residue 470: ALA, Nonterminal, was not found in name map.) (Residue 471: ALA, Nonterminal, was not found in name map.) (Residue 472: GLU, Nonterminal, was not found in name map.) (Residue 473: THR, Nonterminal, was not found in name map.) (Residue 474: HIS, Nonterminal, was not found in name map.) (Residue 475: ASP, Nonterminal, was not found in name map.) (Residue 476: VAL, Nonterminal, was not found in name map.) (Residue 477: TYR, Nonterminal, was not found in name map.) (Residue 478: SER, Nonterminal, was not found in name map.) (Residue 479: TRP, Nonterminal, was not found in name map.) (Residue 480: SER, Nonterminal, was not found in name map.) (Residue 481: PHE, Nonterminal, was not found in name map.) (Residue 482: GLN, Nonterminal, was not found in name map.) (Residue 483: ALA, Nonterminal, was not found in name map.) (Residue 484: SER, Nonterminal, was not found in name map.) (Residue 485: LEU, Nonterminal, was not found in name map.) (Residue 486: PRO, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 487 to: CGLU. (Residue 488: MNG, Terminal/last, was not found in name map.) (Residue 489: CAL, Terminal/last, was not found in name map.) (Residue 490: WYB, Terminal/last, was not found in name map.) (Residue 491: 0fA, Terminal/last, was not found in name map.) (Residue 492: 4YB, Terminal/last, was not found in name map.) (Residue 493: SMB, Terminal/last, was not found in name map.) (Residue 494: 0XB, Terminal/last, was not found in name map.) (Residue 495: 0MA, Terminal/last, was not found in name map.) (Residue 496: 0MA, Terminal/last, was not found in name map.) (Residue 497: 1VA, Terminal/last, was not found in name map.) Joining NVAL - GLU Joining GLU - THR Joining THR - ILE Joining ILE - SER Joining SER - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - GLU Joining GLU - PHE Joining PHE - GLU Joining GLU - PRO Joining PRO - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - ASN Joining ASN - LEU Joining LEU - THR Joining THR - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - THR Joining THR - GLN Joining GLN - SER Joining SER - GLY Joining GLY - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - THR Joining THR - LYS Joining LYS - ILE Joining ILE - ASN Joining ASN - GLN Joining GLN - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ASP Joining ASP - SER Joining SER - THR Joining THR - GLY Joining GLY - ARG Joining ARG - THR Joining THR - LEU Joining LEU - TYR Joining TYR - ALA Joining ALA - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - HIE Joining HIE - ILE Joining ILE - TRP Joining TRP - ASP Joining ASP - MET Joining MET - THR Joining THR - THR Joining THR - GLY Joining GLY - THR Joining THR - VAL Joining VAL - ALA Joining ALA - SER Joining SER - PHE Joining PHE - GLU Joining GLU - THR Joining THR - ARG Joining ARG - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - PRO Joining PRO - TYR Joining TYR - THR Joining THR - ARG Joining ARG - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - ALA Joining ALA - ASP Joining ASP - GLY Joining GLY - LEU Joining LEU - VAL Joining VAL - PHE Joining PHE - PHE Joining PHE - MET Joining MET - GLY Joining GLY - PRO Joining PRO - THR Joining THR - LYS Joining LYS - SER Joining SER - LYS Joining LYS - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PHE Joining PHE - ASN Joining ASN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLN Joining GLN - ASP Joining ASP - ASN Joining ASN - SER Joining SER - TYR Joining TYR - GLN Joining GLN - THR Joining THR - LEU Joining LEU - GLY Joining GLY - VAL Joining VAL - GLU Joining GLU - PHE Joining PHE - ASP Joining ASP - THR Joining THR - PHE Joining PHE - SER Joining SER - ASN Joining ASN - PRO Joining PRO - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - PRO Joining PRO - GLN Joining GLN - VAL Joining VAL - PRO Joining PRO - HIE Joining HIE - ILE Joining ILE - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - VAL Joining VAL - ASN Joining ASN - SER Joining SER - ILE Joining ILE - ARG Joining ARG - SER Joining SER - ILE Joining ILE - LYS Joining LYS - THR Joining THR - GLN Joining GLN - PRO Joining PRO - PHE Joining PHE - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - ILE Joining ILE - LYS Joining LYS - TYR Joining TYR - ASP Joining ASP - ALA Joining ALA - SER Joining SER - SER Joining SER - LYS Joining LYS - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - TYR Joining TYR - PRO Joining PRO - SER Joining SER - SER Joining SER - GLY Joining GLY - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - THR Joining THR - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ILE Joining ILE - VAL Joining VAL - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - GLN Joining GLN - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - TRP Joining TRP - VAL Joining VAL - ASP Joining ASP - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - SER Joining SER - GLY Joining GLY - ALA Joining ALA - THR Joining THR - GLY Joining GLY - ALA Joining ALA - GLN Joining GLN - ARG Joining ARG - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - GLU Joining GLU - THR Joining THR - HIE Joining HIE - ASP Joining ASP - VAL Joining VAL - TYR Joining TYR - SER Joining SER - TRP Joining TRP - SER Joining SER - PHE Joining PHE - GLN Joining GLN - ALA Joining ALA - SER Joining SER - LEU Joining LEU - PRO Joining PRO - CGLU Joining NVAL - GLU Joining GLU - THR Joining THR - ILE Joining ILE - SER Joining SER - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - GLU Joining GLU - PHE Joining PHE - GLU Joining GLU - PRO Joining PRO - GLY Joining GLY - ASN Joining ASN - ASP Joining ASP - ASN Joining ASN - LEU Joining LEU - THR Joining THR - LEU Joining LEU - GLN Joining GLN - GLY Joining GLY - ALA Joining ALA - ALA Joining ALA - LEU Joining LEU - ILE Joining ILE - THR Joining THR - GLN Joining GLN - SER Joining SER - GLY Joining GLY - VAL Joining VAL - LEU Joining LEU - GLN Joining GLN - LEU Joining LEU - THR Joining THR - LYS Joining LYS - ILE Joining ILE - ASN Joining ASN - GLN Joining GLN - ASN Joining ASN - GLY Joining GLY - MET Joining MET - PRO Joining PRO - ALA Joining ALA - TRP Joining TRP - ASP Joining ASP - SER Joining SER - THR Joining THR - GLY Joining GLY - ARG Joining ARG - THR Joining THR - LEU Joining LEU - TYR Joining TYR - ALA Joining ALA - LYS Joining LYS - PRO Joining PRO - VAL Joining VAL - HIE Joining HIE - ILE Joining ILE - TRP Joining TRP - ASP Joining ASP - MET Joining MET - THR Joining THR - THR Joining THR - GLY Joining GLY - THR Joining THR - VAL Joining VAL - ALA Joining ALA - SER Joining SER - PHE Joining PHE - GLU Joining GLU - THR Joining THR - ARG Joining ARG - PHE Joining PHE - SER Joining SER - PHE Joining PHE - SER Joining SER - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - PRO Joining PRO - TYR Joining TYR - THR Joining THR - ARG Joining ARG - PRO Joining PRO - LEU Joining LEU - PRO Joining PRO - ALA Joining ALA - ASP Joining ASP - GLY Joining GLY - LEU Joining LEU - VAL Joining VAL - PHE Joining PHE - PHE Joining PHE - MET Joining MET - GLY Joining GLY - PRO Joining PRO - THR Joining THR - LYS Joining LYS - SER Joining SER - LYS Joining LYS - PRO Joining PRO - ALA Joining ALA - GLN Joining GLN - GLY Joining GLY - TYR Joining TYR - GLY Joining GLY - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - ILE Joining ILE - PHE Joining PHE - ASN Joining ASN - ASN Joining ASN - SER Joining SER - LYS Joining LYS - GLN Joining GLN - ASP Joining ASP - ASN Joining ASN - SER Joining SER - TYR Joining TYR - GLN Joining GLN - THR Joining THR - LEU Joining LEU - GLY Joining GLY - VAL Joining VAL - GLU Joining GLU - PHE Joining PHE - ASP Joining ASP - THR Joining THR - PHE Joining PHE - SER Joining SER - ASN Joining ASN - PRO Joining PRO - TRP Joining TRP - ASP Joining ASP - PRO Joining PRO - PRO Joining PRO - GLN Joining GLN - VAL Joining VAL - PRO Joining PRO - HIE Joining HIE - ILE Joining ILE - GLY Joining GLY - ILE Joining ILE - ASP Joining ASP - VAL Joining VAL - ASN Joining ASN - SER Joining SER - ILE Joining ILE - ARG Joining ARG - SER Joining SER - ILE Joining ILE - LYS Joining LYS - THR Joining THR - GLN Joining GLN - PRO Joining PRO - PHE Joining PHE - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - ASN Joining ASN - GLY Joining GLY - GLN Joining GLN - VAL Joining VAL - ALA Joining ALA - ASN Joining ASN - VAL Joining VAL - VAL Joining VAL - ILE Joining ILE - LYS Joining LYS - TYR Joining TYR - ASP Joining ASP - ALA Joining ALA - SER Joining SER - SER Joining SER - LYS Joining LYS - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - ALA Joining ALA - VAL Joining VAL - LEU Joining LEU - VAL Joining VAL - TYR Joining TYR - PRO Joining PRO - SER Joining SER - SER Joining SER - GLY Joining GLY - ALA Joining ALA - ILE Joining ILE - TYR Joining TYR - THR Joining THR - ILE Joining ILE - ALA Joining ALA - GLU Joining GLU - ILE Joining ILE - VAL Joining VAL - ASP Joining ASP - VAL Joining VAL - LYS Joining LYS - GLN Joining GLN - VAL Joining VAL - LEU Joining LEU - PRO Joining PRO - GLU Joining GLU - TRP Joining TRP - VAL Joining VAL - ASP Joining ASP - VAL Joining VAL - GLY Joining GLY - LEU Joining LEU - SER Joining SER - GLY Joining GLY - ALA Joining ALA - THR Joining THR - GLY Joining GLY - ALA Joining ALA - GLN Joining GLN - ARG Joining ARG - ASP Joining ASP - ALA Joining ALA - ALA Joining ALA - GLU Joining GLU - THR Joining THR - HIE Joining HIE - ASP Joining ASP - VAL Joining VAL - TYR Joining TYR - SER Joining SER - TRP Joining TRP - SER Joining SER - PHE Joining PHE - GLN Joining GLN - ALA Joining ALA - SER Joining SER - LEU Joining LEU - PRO Joining PRO - CGLU total atoms in file: 3990 Leap added 3754 missing atoms according to residue templates: 3754 H / lone pairs > edit ec Unit Editor: Breaking bond: .R.A - .R.A Unit Editor: Breaking bond: .R.A - .R.A Unit Editor: Breaking bond: .R.A - .R.A Unit Editor: Breaking bond: .R<0fA 492>.A - .R<0fA 492>.A Unit Editor: > charge ec Unit Editor: Total unperturbed charge: -12.710158 Unit Editor: Total perturbed charge: -12.710158 Unit Editor: > check ec Unit Editor: Checking 'ec'.... Unit Editor: ERROR: The unperturbed charge of the unit: -12.710158 is not integral. Unit Editor: WARNING: The unperturbed charge of the unit: -12.710158 is not zero. Unit Editor: Warning: Close contact of 1.339978 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.853532 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.915823 angstroms between .R.A and .R<1VA 249>.A Unit Editor: Warning: Close contact of 2.043727 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.230529 angstroms between .R.A and .R<1VA 249>.A Unit Editor: Warning: Close contact of 1.339797 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.851551 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 1.914640 angstroms between .R.A and .R<1VA 498>.A Unit Editor: Warning: Close contact of 2.047499 angstroms between .R.A and .R.A Unit Editor: Warning: Close contact of 2.231033 angstroms between .R.A and .R<1VA 498>.A Unit Editor: Checking parameters for unit 'ec'. Unit Editor: Checking for bond parameters. Unit Editor: Checking for angle parameters. Unit Editor: check: Errors: 1 Warnings: 11 > savepdb ec e2is_glyco.pdb Writing pdb file: e2is_glyco.pdb Converting N-terminal residue name to PDB format: NVAL -> VAL Converting C-terminal residue name to PDB format: CGLU -> GLU Converting N-terminal residue name to PDB format: NVAL -> VAL Converting C-terminal residue name to PDB format: CGLU -> GLU > > saveamberparm ec e2is_g.top e2is_g.crd Checking Unit. ERROR: The unperturbed charge of the unit: -12.710158 is not integral. WARNING: The unperturbed charge of the unit: -12.710158 is not zero. -- ignoring the error and warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 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 old PREP-specified impropers: : C2 C2N N2 H2N : CME N2 C2N O2N <4YB 244>: C2 C2N N2 H2N <4YB 244>: CME N2 C2N O2N <1VA 249>: C2 C2N N2 H2N <1VA 249>: CME N2 C2N O2N : C2 C2N N2 H2N : CME N2 C2N O2N <4YB 493>: C2 C2N N2 H2N <4YB 493>: CME N2 C2N O2N <1VA 498>: C2 C2N N2 H2N <1VA 498>: CME N2 C2N O2N total 1524 improper torsions applied 12 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CGLU 2 NVAL 2 ) (no restraints) > > > solvatebox ec TIP3PBOX 7 Solute vdw bounding box: 64.491 77.562 72.134 Total bounding box for atom centers: 78.491 91.562 86.134 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 5 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 37.548698, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 37.548698, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 37.548698, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 37.548698, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 37.548698, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 18.774349, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 18.774349, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 18.774349, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 18.774349, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 18.774349, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, 0.000000, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, 0.000000, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, 0.000000, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, 0.000000, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, 0.000000, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -18.774349, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -18.774349, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -18.774349, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -18.774349, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -18.774349, -37.548698 Adding box at: x=0 y=4 z=0 Center of solvent box is: 37.548698, -37.548698, 37.548698 Adding box at: x=0 y=4 z=1 Center of solvent box is: 37.548698, -37.548698, 18.774349 Adding box at: x=0 y=4 z=2 Center of solvent box is: 37.548698, -37.548698, 0.000000 Adding box at: x=0 y=4 z=3 Center of solvent box is: 37.548698, -37.548698, -18.774349 Adding box at: x=0 y=4 z=4 Center of solvent box is: 37.548698, -37.548698, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 37.548698, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 37.548698, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 37.548698, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 37.548698, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 37.548698, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 18.774349, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 18.774349, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, 0.000000, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, 0.000000, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -18.774349, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -18.774349, -37.548698 Adding box at: x=1 y=4 z=0 Center of solvent box is: 18.774349, -37.548698, 37.548698 Adding box at: x=1 y=4 z=1 Center of solvent box is: 18.774349, -37.548698, 18.774349 Adding box at: x=1 y=4 z=2 Center of solvent box is: 18.774349, -37.548698, 0.000000 Adding box at: x=1 y=4 z=3 Center of solvent box is: 18.774349, -37.548698, -18.774349 Adding box at: x=1 y=4 z=4 Center of solvent box is: 18.774349, -37.548698, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 37.548698, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 37.548698, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 37.548698, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 37.548698, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 37.548698, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 18.774349, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 18.774349, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, 0.000000, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, 0.000000, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -18.774349, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -18.774349, -37.548698 Adding box at: x=2 y=4 z=0 Center of solvent box is: 0.000000, -37.548698, 37.548698 Adding box at: x=2 y=4 z=1 Center of solvent box is: 0.000000, -37.548698, 18.774349 Adding box at: x=2 y=4 z=2 Center of solvent box is: 0.000000, -37.548698, 0.000000 Adding box at: x=2 y=4 z=3 Center of solvent box is: 0.000000, -37.548698, -18.774349 Adding box at: x=2 y=4 z=4 Center of solvent box is: 0.000000, -37.548698, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 37.548698, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 37.548698, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 37.548698, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 37.548698, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 37.548698, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 18.774349, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 18.774349, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, 0.000000, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, 0.000000, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -18.774349, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -18.774349, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -18.774349, -37.548698 Adding box at: x=3 y=4 z=0 Center of solvent box is: -18.774349, -37.548698, 37.548698 Adding box at: x=3 y=4 z=1 Center of solvent box is: -18.774349, -37.548698, 18.774349 Adding box at: x=3 y=4 z=2 Center of solvent box is: -18.774349, -37.548698, 0.000000 Adding box at: x=3 y=4 z=3 Center of solvent box is: -18.774349, -37.548698, -18.774349 Adding box at: x=3 y=4 z=4 Center of solvent box is: -18.774349, -37.548698, -37.548698 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 37.548698, 37.548698 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 37.548698, 18.774349 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 37.548698, 0.000000 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 37.548698, -18.774349 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 37.548698, -37.548698 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 18.774349, 37.548698 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 18.774349, 18.774349 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 18.774349, 0.000000 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 18.774349, -18.774349 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 18.774349, -37.548698 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, 0.000000, 37.548698 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, 0.000000, 18.774349 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, 0.000000, 0.000000 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, 0.000000, -18.774349 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, 0.000000, -37.548698 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -18.774349, 37.548698 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -18.774349, 18.774349 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -18.774349, 0.000000 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -18.774349, -18.774349 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -18.774349, -37.548698 Adding box at: x=4 y=4 z=0 Center of solvent box is: -37.548698, -37.548698, 37.548698 Adding box at: x=4 y=4 z=1 Center of solvent box is: -37.548698, -37.548698, 18.774349 Adding box at: x=4 y=4 z=2 Center of solvent box is: -37.548698, -37.548698, 0.000000 Adding box at: x=4 y=4 z=3 Center of solvent box is: -37.548698, -37.548698, -18.774349 Adding box at: x=4 y=4 z=4 Center of solvent box is: -37.548698, -37.548698, -37.548698 Total vdw box size: 81.695 94.630 89.316 angstroms. Volume: 690483.422 A^3 Total mass 341705.580 amu, Density 0.822 g/cc Added 15894 residues. > > saveamberparm ec e2is_g_sol.top e2is_g_sol.crd Checking Unit. ERROR: The unperturbed charge of the unit: -12.710158 is not integral. WARNING: The unperturbed charge of the unit: -12.710158 is not zero. -- ignoring the error and warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. 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 old PREP-specified impropers: : C2 C2N N2 H2N : CME N2 C2N O2N <4YB 244>: C2 C2N N2 H2N <4YB 244>: CME N2 C2N O2N <1VA 249>: C2 C2N N2 H2N <1VA 249>: CME N2 C2N O2N : C2 C2N N2 H2N : CME N2 C2N O2N <4YB 493>: C2 C2N N2 H2N <4YB 493>: CME N2 C2N O2N <1VA 498>: C2 C2N N2 H2N <1VA 498>: CME N2 C2N O2N total 1524 improper torsions applied 12 improper torsions in old prep form Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CGLU 2 NVAL 2 WAT 15894 ) (no restraints) > quit Quit