log started: Fri Apr 4 15:20:24 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > 3rg_H = loadmol2 3rg_H.mol2 Loading Mol2 file: ./3rg_H.mol2 Reading MOLECULE named 3rg > 3rg = loadmol2 3rg_H.mol2 Loading Mol2 file: ./3rg_H.mol2 Reading MOLECULE named 3rg > list 3rg 3rg_H gaff > check 3rg_H Checking '3rg_H'.... Checking parameters for unit '3rg_H'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > loadamberparams frcmod Loading parameters: ./frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > saveoff 3rg 3rg.lib Creating 3rg.lib Saving 3rg. Building topology. Building atom parameters. > saveamberparm 3rg 3rg.prmtop 3rg.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 9 improper torsions applied 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 3rg 1 ) (no restraints) > quit Quit log started: Fri Apr 4 15:34:40 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /usr/local/amber12/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /usr/local/amber12/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff ions08.lib Loading library: /usr/local/amber12/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /usr/local/amber12/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 nucleic acids >> # >> 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 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 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" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Apr 4 15:35:18 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > loadamberparams frcmod Loading parameters: ./frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadoff 3rg.lib Loading library: ./3rg.lib Loading: 3rg > complex = loadpdb 1geqc Could not open file 1geqc: not found > complex = loadpdb 1geqc.pdb Loading PDB file: ./1geqc.pdb Enter zPdbReadScan from call depth 0. -- residue 249: duplicate [ C] atoms (total 9) -- residue 249: duplicate [ O] atoms (total 4) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: PHE, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: SER, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: ILE, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: TYR, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: ALA, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: LYS, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ASN, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: LEU, Nonterminal, was not found in name map.) (Residue 26: ALA, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ASP, Nonterminal, was not found in name map.) (Residue 29: GLU, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: ALA, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ALA, Nonterminal, was not found in name map.) (Residue 34: ILE, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: LEU, Nonterminal, was not found in name map.) (Residue 37: GLY, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: ASP, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: ILE, Nonterminal, was not found in name map.) (Residue 45: ALA, Nonterminal, was not found in name map.) (Residue 46: ASP, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: LYS, Nonterminal, was not found in name map.) (Residue 49: THR, Nonterminal, was not found in name map.) (Residue 50: ILE, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: HIS, Nonterminal, was not found in name map.) (Residue 55: TYR, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: ALA, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: ARG, Nonterminal, was not found in name map.) (Residue 66: GLU, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: PHE, Nonterminal, was not found in name map.) (Residue 69: TRP, Nonterminal, was not found in name map.) (Residue 70: ILE, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: GLU, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: ARG, Nonterminal, was not found in name map.) (Residue 76: ARG, Nonterminal, was not found in name map.) (Residue 77: HIS, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: SER, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: PRO, Nonterminal, was not found in name map.) (Residue 82: ILE, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: LEU, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: THR, Nonterminal, was not found in name map.) (Residue 87: TYR, Nonterminal, was not found in name map.) (Residue 88: TYR, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: PRO, Nonterminal, was not found in name map.) (Residue 91: ILE, Nonterminal, was not found in name map.) (Residue 92: TYR, Nonterminal, was not found in name map.) (Residue 93: ARG, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLY, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ASN, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: LEU, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: GLU, Nonterminal, was not found in name map.) (Residue 103: ALA, Nonterminal, was not found in name map.) (Residue 104: LYS, Nonterminal, was not found in name map.) (Residue 105: ALA, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: GLY, Nonterminal, was not found in name map.) (Residue 108: VAL, Nonterminal, was not found in name map.) (Residue 109: ASP, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: ILE, Nonterminal, was not found in name map.) (Residue 112: LEU, Nonterminal, was not found in name map.) (Residue 113: VAL, Nonterminal, was not found in name map.) (Residue 114: VAL, Nonterminal, was not found in name map.) (Residue 115: ASP, Nonterminal, was not found in name map.) (Residue 116: LEU, Nonterminal, was not found in name map.) (Residue 117: PRO, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: HIS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: LYS, Nonterminal, was not found in name map.) (Residue 123: GLU, Nonterminal, was not found in name map.) (Residue 124: PHE, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: GLU, Nonterminal, was not found in name map.) (Residue 127: ILE, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ARG, Nonterminal, was not found in name map.) (Residue 130: GLU, Nonterminal, was not found in name map.) (Residue 131: GLU, Nonterminal, was not found in name map.) (Residue 132: GLY, Nonterminal, was not found in name map.) (Residue 133: ILE, Nonterminal, was not found in name map.) (Residue 134: LYS, Nonterminal, was not found in name map.) (Residue 135: THR, Nonterminal, was not found in name map.) (Residue 136: VAL, Nonterminal, was not found in name map.) (Residue 137: PHE, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: PRO, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: GLU, Nonterminal, was not found in name map.) (Residue 147: ARG, Nonterminal, was not found in name map.) (Residue 148: LEU, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: VAL, Nonterminal, was not found in name map.) (Residue 151: ILE, Nonterminal, was not found in name map.) (Residue 152: ASP, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: MET, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: PHE, Nonterminal, was not found in name map.) (Residue 159: VAL, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: LEU, Nonterminal, was not found in name map.) (Residue 162: VAL, Nonterminal, was not found in name map.) (Residue 163: SER, Nonterminal, was not found in name map.) (Residue 164: LEU, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: GLY, Nonterminal, was not found in name map.) (Residue 167: THR, Nonterminal, was not found in name map.) (Residue 168: THR, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: ALA, Nonterminal, was not found in name map.) (Residue 171: ARG, Nonterminal, was not found in name map.) (Residue 172: GLU, Nonterminal, was not found in name map.) (Residue 173: GLU, Nonterminal, was not found in name map.) (Residue 174: ILE, Nonterminal, was not found in name map.) (Residue 175: PRO, Nonterminal, was not found in name map.) (Residue 176: LYS, Nonterminal, was not found in name map.) (Residue 177: THR, Nonterminal, was not found in name map.) (Residue 178: ALA, Nonterminal, was not found in name map.) (Residue 179: TYR, Nonterminal, was not found in name map.) (Residue 180: ASP, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: ARG, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: ALA, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: ILE, Nonterminal, was not found in name map.) (Residue 189: CYS, Nonterminal, was not found in name map.) (Residue 190: ARG, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: LYS, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: ALA, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: PHE, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: VAL, Nonterminal, was not found in name map.) (Residue 200: SER, Nonterminal, was not found in name map.) (Residue 201: LYS, Nonterminal, was not found in name map.) (Residue 202: ARG, Nonterminal, was not found in name map.) (Residue 203: GLU, Nonterminal, was not found in name map.) (Residue 204: HIS, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: SER, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: LEU, Nonterminal, was not found in name map.) (Residue 210: LYS, Nonterminal, was not found in name map.) (Residue 211: GLU, Nonterminal, was not found in name map.) (Residue 212: GLY, Nonterminal, was not found in name map.) (Residue 213: ALA, Nonterminal, was not found in name map.) (Residue 214: ASN, Nonterminal, was not found in name map.) (Residue 215: GLY, Nonterminal, was not found in name map.) (Residue 216: VAL, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: VAL, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: LEU, Nonterminal, was not found in name map.) (Residue 223: VAL, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ILE, Nonterminal, was not found in name map.) (Residue 227: GLY, Nonterminal, was not found in name map.) (Residue 228: GLU, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLY, Nonterminal, was not found in name map.) (Residue 231: ARG, Nonterminal, was not found in name map.) (Residue 232: GLU, Nonterminal, was not found in name map.) (Residue 233: ALA, Nonterminal, was not found in name map.) (Residue 234: THR, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: PHE, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: LYS, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: GLU, Nonterminal, was not found in name map.) (Residue 243: GLU, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: GLY, Nonterminal, was not found in name map.) Mapped residue ILE, term: Terminal/last, seq. number: 247 to: CILE. (Residue 248: 3rg, Terminal/last, was not found in name map.) Created a new atom named: HN1 within residue: .R Created a new atom named: HN2 within residue: .R Created a new atom named: HN3 within residue: .R Joining NMET - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - LYS Created a new atom named: HN within residue: .R Joining LYS - GLN Created a new atom named: HN within residue: .R Joining GLN - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - TYR Created a new atom named: HN within residue: .R Joining TYR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ILE Created a new atom named: HN within residue: .R Joining ILE - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - PHE Created a new atom named: HN within residue: .R Joining PHE - SER Created a new atom named: HN within residue: .R Joining SER - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ILE Created a new atom named: HN within residue: .R Joining ILE - GLN Created a new atom named: HN within residue: .R Joining GLN - GLU Created a new atom named: HN within residue: .R Joining GLU - SER Created a new atom named: HN within residue: .R Joining SER - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - PHE Created a new atom named: HN within residue: .R Joining PHE - TRP Created a new atom named: HN within residue: .R Joining TRP - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - SER Created a new atom named: HN within residue: .R Joining SER - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - TYR Created a new atom named: HN within residue: .R Joining TYR - TYR Created a new atom named: HN within residue: .R Joining TYR - ASN Created a new atom named: HN within residue: .R Joining ASN - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - ALA Created a new atom named: HN within residue: .R Joining ALA - PRO Joining PRO - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - ARG Created a new atom named: HN within residue: .R Joining ARG - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ILE Created a new atom named: HN within residue: .R Joining ILE - ASP Created a new atom named: HN within residue: .R Joining ASP - ASP Created a new atom named: HN within residue: .R Joining ASP - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - VAL Created a new atom named: HN within residue: .R Joining VAL - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - TYR Created a new atom named: HN within residue: .R Joining TYR - GLY Created a new atom named: HN within residue: .R Joining GLY - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - TYR Created a new atom named: HN within residue: .R Joining TYR - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ILE Created a new atom named: HN within residue: .R Joining ILE - CYS Created a new atom named: HN within residue: .R Joining CYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ALA Created a new atom named: HN within residue: .R Joining ALA - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - ILE Created a new atom named: HN within residue: .R Joining ILE - ILE Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLU Created a new atom named: HN within residue: .R Joining GLU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLY Created a new atom named: HN within residue: .R Joining GLY - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - CILE Created a new atom named: HN within residue: .R Created a new atom named: C within residue: .R<3rg 249> Created a new atom named: N within residue: .R<3rg 249> Created a new atom named: O within residue: .R<3rg 249> Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A Added missing heavy atom: .R<3rg 249>.A total atoms in file: 2392 Leap added 1829 missing atoms according to residue templates: 14 Heavy 1815 H / lone pairs The file contained 247 atoms not in residue templates > saveamberparm complex 1deqc.prmtop 1geqc.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 2.999000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. 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FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. Failed to generate parameters Parameter file was not saved. > addions 1geqc Cl- 3 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions 1geqc Cl- -3 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions 1geqc Cl- -2 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions 1geqc Cl- 2 addIons: Argument #1 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addions, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. log started: Fri Apr 4 15:39:08 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /usr/local/amber12/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /usr/local/amber12/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff ions08.lib Loading library: /usr/local/amber12/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /usr/local/amber12/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 nucleic acids >> # >> 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 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 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" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > complex= loadpdb 1geqc.pdb Loading PDB file: ./1geqc.pdb Enter zPdbReadScan from call depth 0. -- residue 249: duplicate [ C] atoms (total 9) -- residue 249: duplicate [ O] atoms (total 4) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: PHE, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: SER, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: ILE, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: TYR, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: ALA, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: LYS, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ASN, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: LEU, Nonterminal, was not found in name map.) (Residue 26: ALA, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ASP, Nonterminal, was not found in name map.) (Residue 29: GLU, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: ALA, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ALA, Nonterminal, was not found in name map.) (Residue 34: ILE, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: LEU, Nonterminal, was not found in name map.) (Residue 37: GLY, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: ASP, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: ILE, Nonterminal, was not found in name map.) (Residue 45: ALA, Nonterminal, was not found in name map.) (Residue 46: ASP, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: LYS, Nonterminal, was not found in name map.) (Residue 49: THR, Nonterminal, was not found in name map.) (Residue 50: ILE, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: HIS, Nonterminal, was not found in name map.) (Residue 55: TYR, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: ALA, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: ARG, Nonterminal, was not found in name map.) (Residue 66: GLU, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: PHE, Nonterminal, was not found in name map.) (Residue 69: TRP, Nonterminal, was not found in name map.) (Residue 70: ILE, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: GLU, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: ARG, Nonterminal, was not found in name map.) (Residue 76: ARG, Nonterminal, was not found in name map.) (Residue 77: HIS, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: SER, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: PRO, Nonterminal, was not found in name map.) (Residue 82: ILE, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: LEU, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: THR, Nonterminal, was not found in name map.) (Residue 87: TYR, Nonterminal, was not found in name map.) (Residue 88: TYR, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: PRO, Nonterminal, was not found in name map.) (Residue 91: ILE, Nonterminal, was not found in name map.) (Residue 92: TYR, Nonterminal, was not found in name map.) (Residue 93: ARG, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLY, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ASN, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: LEU, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: GLU, Nonterminal, was not found in name map.) (Residue 103: ALA, Nonterminal, was not found in name map.) (Residue 104: LYS, Nonterminal, was not found in name map.) (Residue 105: ALA, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: GLY, Nonterminal, was not found in name map.) (Residue 108: VAL, Nonterminal, was not found in name map.) (Residue 109: ASP, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: ILE, Nonterminal, was not found in name map.) (Residue 112: LEU, Nonterminal, was not found in name map.) (Residue 113: VAL, Nonterminal, was not found in name map.) (Residue 114: VAL, Nonterminal, was not found in name map.) (Residue 115: ASP, Nonterminal, was not found in name map.) (Residue 116: LEU, Nonterminal, was not found in name map.) (Residue 117: PRO, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: HIS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: LYS, Nonterminal, was not found in name map.) (Residue 123: GLU, Nonterminal, was not found in name map.) (Residue 124: PHE, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: GLU, Nonterminal, was not found in name map.) (Residue 127: ILE, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ARG, Nonterminal, was not found in name map.) (Residue 130: GLU, Nonterminal, was not found in name map.) (Residue 131: GLU, Nonterminal, was not found in name map.) (Residue 132: GLY, Nonterminal, was not found in name map.) (Residue 133: ILE, Nonterminal, was not found in name map.) (Residue 134: LYS, Nonterminal, was not found in name map.) (Residue 135: THR, Nonterminal, was not found in name map.) (Residue 136: VAL, Nonterminal, was not found in name map.) (Residue 137: PHE, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: PRO, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: GLU, Nonterminal, was not found in name map.) (Residue 147: ARG, Nonterminal, was not found in name map.) (Residue 148: LEU, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: VAL, Nonterminal, was not found in name map.) (Residue 151: ILE, Nonterminal, was not found in name map.) (Residue 152: ASP, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: MET, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: PHE, Nonterminal, was not found in name map.) (Residue 159: VAL, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: LEU, Nonterminal, was not found in name map.) (Residue 162: VAL, Nonterminal, was not found in name map.) (Residue 163: SER, Nonterminal, was not found in name map.) (Residue 164: LEU, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: GLY, Nonterminal, was not found in name map.) (Residue 167: THR, Nonterminal, was not found in name map.) (Residue 168: THR, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: ALA, Nonterminal, was not found in name map.) (Residue 171: ARG, Nonterminal, was not found in name map.) (Residue 172: GLU, Nonterminal, was not found in name map.) (Residue 173: GLU, Nonterminal, was not found in name map.) (Residue 174: ILE, Nonterminal, was not found in name map.) (Residue 175: PRO, Nonterminal, was not found in name map.) (Residue 176: LYS, Nonterminal, was not found in name map.) (Residue 177: THR, Nonterminal, was not found in name map.) (Residue 178: ALA, Nonterminal, was not found in name map.) (Residue 179: TYR, Nonterminal, was not found in name map.) (Residue 180: ASP, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: ARG, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: ALA, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: ILE, Nonterminal, was not found in name map.) (Residue 189: CYS, Nonterminal, was not found in name map.) (Residue 190: ARG, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: LYS, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: ALA, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: PHE, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: VAL, Nonterminal, was not found in name map.) (Residue 200: SER, Nonterminal, was not found in name map.) (Residue 201: LYS, Nonterminal, was not found in name map.) (Residue 202: ARG, Nonterminal, was not found in name map.) (Residue 203: GLU, Nonterminal, was not found in name map.) (Residue 204: HIS, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: SER, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: LEU, Nonterminal, was not found in name map.) (Residue 210: LYS, Nonterminal, was not found in name map.) (Residue 211: GLU, Nonterminal, was not found in name map.) (Residue 212: GLY, Nonterminal, was not found in name map.) (Residue 213: ALA, Nonterminal, was not found in name map.) (Residue 214: ASN, Nonterminal, was not found in name map.) (Residue 215: GLY, Nonterminal, was not found in name map.) (Residue 216: VAL, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: VAL, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: LEU, Nonterminal, was not found in name map.) (Residue 223: VAL, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ILE, Nonterminal, was not found in name map.) (Residue 227: GLY, Nonterminal, was not found in name map.) (Residue 228: GLU, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLY, Nonterminal, was not found in name map.) (Residue 231: ARG, Nonterminal, was not found in name map.) (Residue 232: GLU, Nonterminal, was not found in name map.) (Residue 233: ALA, Nonterminal, was not found in name map.) (Residue 234: THR, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: PHE, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: LYS, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: GLU, Nonterminal, was not found in name map.) (Residue 243: GLU, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: GLY, Nonterminal, was not found in name map.) Mapped residue ILE, term: Terminal/last, seq. number: 247 to: CILE. (Residue 248: 3rg, Terminal/last, was not found in name map.) Unknown residue: 3rg number: 248 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Created a new atom named: HN1 within residue: .R Created a new atom named: HN2 within residue: .R Created a new atom named: HN3 within residue: .R Joining NMET - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - LYS Created a new atom named: HN within residue: .R Joining LYS - GLN Created a new atom named: HN within residue: .R Joining GLN - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - TYR Created a new atom named: HN within residue: .R Joining TYR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ILE Created a new atom named: HN within residue: .R Joining ILE - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - PHE Created a new atom named: HN within residue: .R Joining PHE - SER Created a new atom named: HN within residue: .R Joining SER - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ILE Created a new atom named: HN within residue: .R Joining ILE - GLN Created a new atom named: HN within residue: .R Joining GLN - GLU Created a new atom named: HN within residue: .R Joining GLU - SER Created a new atom named: HN within residue: .R Joining SER - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - PHE Created a new atom named: HN within residue: .R Joining PHE - TRP Created a new atom named: HN within residue: .R Joining TRP - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - SER Created a new atom named: HN within residue: .R Joining SER - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - TYR Created a new atom named: HN within residue: .R Joining TYR - TYR Created a new atom named: HN within residue: .R Joining TYR - ASN Created a new atom named: HN within residue: .R Joining ASN - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - ALA Created a new atom named: HN within residue: .R Joining ALA - PRO Joining PRO - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - ARG Created a new atom named: HN within residue: .R Joining ARG - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ILE Created a new atom named: HN within residue: .R Joining ILE - ASP Created a new atom named: HN within residue: .R Joining ASP - ASP Created a new atom named: HN within residue: .R Joining ASP - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - VAL Created a new atom named: HN within residue: .R Joining VAL - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - TYR Created a new atom named: HN within residue: .R Joining TYR - GLY Created a new atom named: HN within residue: .R Joining GLY - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - TYR Created a new atom named: HN within residue: .R Joining TYR - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ILE Created a new atom named: HN within residue: .R Joining ILE - CYS Created a new atom named: HN within residue: .R Joining CYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ALA Created a new atom named: HN within residue: .R Joining ALA - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - ILE Created a new atom named: HN within residue: .R Joining ILE - ILE Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLU Created a new atom named: HN within residue: .R Joining GLU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLY Created a new atom named: HN within residue: .R Joining GLY - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - CILE Created a new atom named: HN within residue: .R Creating new UNIT for residue: 3rg sequence: 249 Created a new atom named: C within residue: .R<3rg 249> Created a new atom named: N within residue: .R<3rg 249> Created a new atom named: O within residue: .R<3rg 249> total atoms in file: 2392 Leap added 1806 missing atoms according to residue templates: 1806 H / lone pairs The file contained 247 atoms not in residue templates > saveamberparm complex 1geqc.prmtop 1geqc.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 3.000000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. Failed to generate parameters Parameter file was not saved. > charge 1geqc charge: Argument #1 is type String must be of type: [unit molecule residue atom list] usage: charge > charge 1geqc charge: Argument #1 is type String must be of type: [unit molecule residue atom list] usage: charge > charge 1geqc.pdb charge: Argument #1 is type String must be of type: [unit molecule residue atom list] usage: charge log started: Fri Apr 4 15:43:16 2014 Log file: ./leap.log > # > # ----- leaprc for loading the ff12SB force field > # ----- NOTE: this is designed for PDB format 3! > # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "HZ" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OP" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CX" "C" "sp3" } > { "C8" "C" "sp3" } > { "2C" "C" "sp3" } > { "3C" "C" "sp3" } > { "CH" "C" "sp3" } > { "CS" "C" "sp2" } > { "C" "C" "sp2" } > { "CO" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "C5" "C" "sp2" } > { "C4" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp3" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "Ca" "sp3" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "NY" "N" "sp2" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "EP" "" "sp3" } > { "F" "F" "sp3" } > { "Cl" "Cl" "sp3" } > { "Br" "Br" "sp3" } > { "I" "I" "sp3" } > { "F-" "F" "sp3" } > { "Cl-" "Cl" "sp3" } > { "Br-" "Br" "sp3" } > { "I-" "I" "sp3" } > { "Li+" "Li" "sp3" } > { "Na+" "Na" "sp3" } > { "K+" "K" "sp3" } > { "Rb+" "Rb" "sp3" } > { "Cs+" "Cs" "sp3" } > { "Mg+" "Mg" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters > # > # Load main chain and terminating amino acid libraries, nucleic acids > # > loadOff amino12.lib Loading library: /usr/local/amber12/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > loadOff aminoct12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME > loadOff aminont12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > loadOff nucleic12.lib Loading library: /usr/local/amber12/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN > # > # Load water and ions > # > loadOff ions08.lib Loading library: /usr/local/amber12/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ > loadOff solvents.lib Loading library: /usr/local/amber12/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 nucleic acids > # > 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 "G" "G5" } { 1 "G" "G3" } > { 0 "A" "A5" } { 1 "A" "A3" } > { 0 "C" "C5" } { 1 "C" "C3" } > { 0 "U" "U5" } { 1 "U" "U3" } > { 0 "DG" "DG5" } { 1 "DG" "DG3" } > { 0 "DA" "DA5" } { 1 "DA" "DA3" } > { 0 "DC" "DC5" } { 1 "DC" "DC3" } > { 0 "DT" "DT5" } { 1 "DT" "DT3" } > # some old Amber residue names for RNA: > { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } > { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } > { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } > { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } > # some really old Amber residue names, assuming DNA: > { 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" } > # uncomment out the following if you have this old style RNA files: > # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } > # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } > # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } > # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } > > } > > # try to be good about reading in really old atom names as well: > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "O2*" "O2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "H1*" "H1'" } > { "H2*1" "H2'" } > { "H2*2" "H2''" } > { "H2'1" "H2'" } > { "H2'2" "H2''" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'" } > { "H5*2" "H5''" } > { "H5'1" "H5'" } > { "H5'2" "H5''" } > { "HO'2" "HO2'" } > { "H5T" "HO5'" } > { "H3T" "HO3'" } > { "O1'" "O4'" } > { "OA" "OP1" } > { "OB" "OP2" } > { "O1P" "OP1" } > { "O2P" "OP2" } > } > > # > # assume that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > source leaprc.gaff ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Apr 4 15:43:26 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > 3rg_H = loadmol2 3rg_H.mol2 Loading Mol2 file: ./3rg_H.mol2 Reading MOLECULE named 3rg > check 3rg_H Checking '3rg_H'.... Checking parameters for unit '3rg_H'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > loadamberparams 3rg_H.frcmod Loading parameters: ./3rg_H.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > save0ff 3rg_H 3rg_H.lib ERROR: syntax error > saveoff 3rg_H 3rg_H.lib Creating 3rg_H.lib Saving 3rg_H. Building topology. Building atom parameters. > saveamberparm 3rg_H 3rg_H.prmtop 3rg_H.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 9 improper torsions applied 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 3rg 1 ) (no restraints) > source leaprc.ff12SB ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.ff12SB ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.ff12SB done >> logFile leap.log log started: Fri Apr 4 15:47:26 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /usr/local/amber12/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /usr/local/amber12/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /usr/local/amber12/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff ions08.lib Loading library: /usr/local/amber12/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /usr/local/amber12/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 nucleic acids >> # >> 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 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 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" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >> >> } Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS Substituting map 0G -> G5 for 0G -> G5 Substituting map 1G -> G3 for 1G -> G3 Substituting map 0A -> A5 for 0A -> A5 Substituting map 1A -> A3 for 1A -> A3 Substituting map 0C -> C5 for 0C -> C5 Substituting map 1C -> C3 for 1C -> C3 Substituting map 0U -> U5 for 0U -> U5 Substituting map 1U -> U3 for 1U -> U3 Substituting map 0DG -> DG5 for 0DG -> DG5 Substituting map 1DG -> DG3 for 1DG -> DG3 Substituting map 0DA -> DA5 for 0DA -> DA5 Substituting map 1DA -> DA3 for 1DA -> DA3 Substituting map 0DC -> DC5 for 0DC -> DC5 Substituting map 1DC -> DC3 for 1DC -> DC3 Substituting map 0DT -> DT5 for 0DT -> DT5 Substituting map 1DT -> DT3 for 1DT -> DT3 Substituting map 0RA5 -> A5 for 0RA5 -> A5 Substituting map 1RA3 -> A3 for 1RA3 -> A3 Substituting map RA -> A for RA -> A Substituting map 0RC5 -> C5 for 0RC5 -> C5 Substituting map 1RC3 -> C3 for 1RC3 -> C3 Substituting map RC -> C for RC -> C Substituting map 0RG5 -> G5 for 0RG5 -> G5 Substituting map 1RG3 -> G3 for 1RG3 -> G3 Substituting map RG -> G for RG -> G Substituting map 0RU5 -> U5 for 0RU5 -> U5 Substituting map 1RU3 -> U3 for 1RU3 -> U3 Substituting map RU -> U for RU -> U Substituting map 0GUA -> DG5 for 0GUA -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map O2* -> O2' for O2* -> O2' Substituting map C1* -> C1' for C1* -> C1' Substituting map C5M -> C7 for C5M -> C7 Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2' for H2*1 -> H2' Substituting map H2*2 -> H2'' for H2*2 -> H2'' Substituting map H2'1 -> H2' for H2'1 -> H2' Substituting map H2'2 -> H2'' for H2'2 -> H2'' Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5' for H5*1 -> H5' Substituting map H5*2 -> H5'' for H5*2 -> H5'' Substituting map H5'1 -> H5' for H5'1 -> H5' Substituting map H5'2 -> H5'' for H5'2 -> H5'' Substituting map HO'2 -> HO2' for HO'2 -> HO2' Substituting map H5T -> HO5' for H5T -> HO5' Substituting map H3T -> HO3' for H3T -> HO3' Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> OP1 for OA -> OP1 Substituting map OB -> OP2 for OB -> OP2 Substituting map O1P -> OP1 for O1P -> OP1 Substituting map O2P -> OP2 for O2P -> OP2 >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Fri Apr 4 15:47:46 2014 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end (UNKNOWN ATOM TYPE: cz) > > loadamberparams 3rg_H.frcmod Loading parameters: ./3rg_H.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadoff 3rg_H.lib Loading library: ./3rg_H.lib Loading: 3rg_H > complex = loadpdb 1geqc.pdb Loading PDB file: ./1geqc.pdb Enter zPdbReadScan from call depth 0. -- residue 249: duplicate [ C] atoms (total 9) -- residue 249: duplicate [ O] atoms (total 4) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: PHE, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: ASP, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: SER, Nonterminal, was not found in name map.) (Residue 6: LEU, Nonterminal, was not found in name map.) (Residue 7: ILE, Nonterminal, was not found in name map.) (Residue 8: PRO, Nonterminal, was not found in name map.) (Residue 9: TYR, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: THR, Nonterminal, was not found in name map.) (Residue 12: ALA, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: ASP, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: ASP, Nonterminal, was not found in name map.) (Residue 17: LYS, Nonterminal, was not found in name map.) (Residue 18: GLN, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: THR, Nonterminal, was not found in name map.) (Residue 21: LEU, Nonterminal, was not found in name map.) (Residue 22: ASN, Nonterminal, was not found in name map.) (Residue 23: PHE, Nonterminal, was not found in name map.) (Residue 24: LEU, Nonterminal, was not found in name map.) (Residue 25: LEU, Nonterminal, was not found in name map.) (Residue 26: ALA, Nonterminal, was not found in name map.) (Residue 27: LEU, Nonterminal, was not found in name map.) (Residue 28: ASP, Nonterminal, was not found in name map.) (Residue 29: GLU, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: ALA, Nonterminal, was not found in name map.) (Residue 32: GLY, Nonterminal, was not found in name map.) (Residue 33: ALA, Nonterminal, was not found in name map.) (Residue 34: ILE, Nonterminal, was not found in name map.) (Residue 35: GLU, Nonterminal, was not found in name map.) (Residue 36: LEU, Nonterminal, was not found in name map.) (Residue 37: GLY, Nonterminal, was not found in name map.) (Residue 38: ILE, Nonterminal, was not found in name map.) (Residue 39: PRO, Nonterminal, was not found in name map.) (Residue 40: PHE, Nonterminal, was not found in name map.) (Residue 41: SER, Nonterminal, was not found in name map.) (Residue 42: ASP, Nonterminal, was not found in name map.) (Residue 43: PRO, Nonterminal, was not found in name map.) (Residue 44: ILE, Nonterminal, was not found in name map.) (Residue 45: ALA, Nonterminal, was not found in name map.) (Residue 46: ASP, Nonterminal, was not found in name map.) (Residue 47: GLY, Nonterminal, was not found in name map.) (Residue 48: LYS, Nonterminal, was not found in name map.) (Residue 49: THR, Nonterminal, was not found in name map.) (Residue 50: ILE, Nonterminal, was not found in name map.) (Residue 51: GLN, Nonterminal, was not found in name map.) (Residue 52: GLU, Nonterminal, was not found in name map.) (Residue 53: SER, Nonterminal, was not found in name map.) (Residue 54: HIS, Nonterminal, was not found in name map.) (Residue 55: TYR, Nonterminal, was not found in name map.) (Residue 56: ARG, Nonterminal, was not found in name map.) (Residue 57: ALA, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: ASN, Nonterminal, was not found in name map.) (Residue 61: GLY, Nonterminal, was not found in name map.) (Residue 62: PHE, Nonterminal, was not found in name map.) (Residue 63: LYS, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: ARG, Nonterminal, was not found in name map.) (Residue 66: GLU, Nonterminal, was not found in name map.) (Residue 67: ALA, Nonterminal, was not found in name map.) (Residue 68: PHE, Nonterminal, was not found in name map.) (Residue 69: TRP, Nonterminal, was not found in name map.) (Residue 70: ILE, Nonterminal, was not found in name map.) (Residue 71: VAL, Nonterminal, was not found in name map.) (Residue 72: LYS, Nonterminal, was not found in name map.) (Residue 73: GLU, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: ARG, Nonterminal, was not found in name map.) (Residue 76: ARG, Nonterminal, was not found in name map.) (Residue 77: HIS, Nonterminal, was not found in name map.) (Residue 78: SER, Nonterminal, was not found in name map.) (Residue 79: SER, Nonterminal, was not found in name map.) (Residue 80: THR, Nonterminal, was not found in name map.) (Residue 81: PRO, Nonterminal, was not found in name map.) (Residue 82: ILE, Nonterminal, was not found in name map.) (Residue 83: VAL, Nonterminal, was not found in name map.) (Residue 84: LEU, Nonterminal, was not found in name map.) (Residue 85: MET, Nonterminal, was not found in name map.) (Residue 86: THR, Nonterminal, was not found in name map.) (Residue 87: TYR, Nonterminal, was not found in name map.) (Residue 88: TYR, Nonterminal, was not found in name map.) (Residue 89: ASN, Nonterminal, was not found in name map.) (Residue 90: PRO, Nonterminal, was not found in name map.) (Residue 91: ILE, Nonterminal, was not found in name map.) (Residue 92: TYR, Nonterminal, was not found in name map.) (Residue 93: ARG, Nonterminal, was not found in name map.) (Residue 94: ALA, Nonterminal, was not found in name map.) (Residue 95: GLY, Nonterminal, was not found in name map.) (Residue 96: VAL, Nonterminal, was not found in name map.) (Residue 97: ARG, Nonterminal, was not found in name map.) (Residue 98: ASN, Nonterminal, was not found in name map.) (Residue 99: PHE, Nonterminal, was not found in name map.) (Residue 100: LEU, Nonterminal, was not found in name map.) (Residue 101: ALA, Nonterminal, was not found in name map.) (Residue 102: GLU, Nonterminal, was not found in name map.) (Residue 103: ALA, Nonterminal, was not found in name map.) (Residue 104: LYS, Nonterminal, was not found in name map.) (Residue 105: ALA, Nonterminal, was not found in name map.) (Residue 106: SER, Nonterminal, was not found in name map.) (Residue 107: GLY, Nonterminal, was not found in name map.) (Residue 108: VAL, Nonterminal, was not found in name map.) (Residue 109: ASP, Nonterminal, was not found in name map.) (Residue 110: GLY, Nonterminal, was not found in name map.) (Residue 111: ILE, Nonterminal, was not found in name map.) (Residue 112: LEU, Nonterminal, was not found in name map.) (Residue 113: VAL, Nonterminal, was not found in name map.) (Residue 114: VAL, Nonterminal, was not found in name map.) (Residue 115: ASP, Nonterminal, was not found in name map.) (Residue 116: LEU, Nonterminal, was not found in name map.) (Residue 117: PRO, Nonterminal, was not found in name map.) (Residue 118: VAL, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: HIS, Nonterminal, was not found in name map.) (Residue 121: ALA, Nonterminal, was not found in name map.) (Residue 122: LYS, Nonterminal, was not found in name map.) (Residue 123: GLU, Nonterminal, was not found in name map.) (Residue 124: PHE, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: GLU, Nonterminal, was not found in name map.) (Residue 127: ILE, Nonterminal, was not found in name map.) (Residue 128: ALA, Nonterminal, was not found in name map.) (Residue 129: ARG, Nonterminal, was not found in name map.) (Residue 130: GLU, Nonterminal, was not found in name map.) (Residue 131: GLU, Nonterminal, was not found in name map.) (Residue 132: GLY, Nonterminal, was not found in name map.) (Residue 133: ILE, Nonterminal, was not found in name map.) (Residue 134: LYS, Nonterminal, was not found in name map.) (Residue 135: THR, Nonterminal, was not found in name map.) (Residue 136: VAL, Nonterminal, was not found in name map.) (Residue 137: PHE, Nonterminal, was not found in name map.) (Residue 138: LEU, Nonterminal, was not found in name map.) (Residue 139: ALA, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: PRO, Nonterminal, was not found in name map.) (Residue 142: ASN, Nonterminal, was not found in name map.) (Residue 143: THR, Nonterminal, was not found in name map.) (Residue 144: PRO, Nonterminal, was not found in name map.) (Residue 145: ASP, Nonterminal, was not found in name map.) (Residue 146: GLU, Nonterminal, was not found in name map.) (Residue 147: ARG, Nonterminal, was not found in name map.) (Residue 148: LEU, Nonterminal, was not found in name map.) (Residue 149: LYS, Nonterminal, was not found in name map.) (Residue 150: VAL, Nonterminal, was not found in name map.) (Residue 151: ILE, Nonterminal, was not found in name map.) (Residue 152: ASP, Nonterminal, was not found in name map.) (Residue 153: ASP, Nonterminal, was not found in name map.) (Residue 154: MET, Nonterminal, was not found in name map.) (Residue 155: THR, Nonterminal, was not found in name map.) (Residue 156: THR, Nonterminal, was not found in name map.) (Residue 157: GLY, Nonterminal, was not found in name map.) (Residue 158: PHE, Nonterminal, was not found in name map.) (Residue 159: VAL, Nonterminal, was not found in name map.) (Residue 160: TYR, Nonterminal, was not found in name map.) (Residue 161: LEU, Nonterminal, was not found in name map.) (Residue 162: VAL, Nonterminal, was not found in name map.) (Residue 163: SER, Nonterminal, was not found in name map.) (Residue 164: LEU, Nonterminal, was not found in name map.) (Residue 165: TYR, Nonterminal, was not found in name map.) (Residue 166: GLY, Nonterminal, was not found in name map.) (Residue 167: THR, Nonterminal, was not found in name map.) (Residue 168: THR, Nonterminal, was not found in name map.) (Residue 169: GLY, Nonterminal, was not found in name map.) (Residue 170: ALA, Nonterminal, was not found in name map.) (Residue 171: ARG, Nonterminal, was not found in name map.) (Residue 172: GLU, Nonterminal, was not found in name map.) (Residue 173: GLU, Nonterminal, was not found in name map.) (Residue 174: ILE, Nonterminal, was not found in name map.) (Residue 175: PRO, Nonterminal, was not found in name map.) (Residue 176: LYS, Nonterminal, was not found in name map.) (Residue 177: THR, Nonterminal, was not found in name map.) (Residue 178: ALA, Nonterminal, was not found in name map.) (Residue 179: TYR, Nonterminal, was not found in name map.) (Residue 180: ASP, Nonterminal, was not found in name map.) (Residue 181: LEU, Nonterminal, was not found in name map.) (Residue 182: LEU, Nonterminal, was not found in name map.) (Residue 183: ARG, Nonterminal, was not found in name map.) (Residue 184: ARG, Nonterminal, was not found in name map.) (Residue 185: ALA, Nonterminal, was not found in name map.) (Residue 186: LYS, Nonterminal, was not found in name map.) (Residue 187: ARG, Nonterminal, was not found in name map.) (Residue 188: ILE, Nonterminal, was not found in name map.) (Residue 189: CYS, Nonterminal, was not found in name map.) (Residue 190: ARG, Nonterminal, was not found in name map.) (Residue 191: ASN, Nonterminal, was not found in name map.) (Residue 192: LYS, Nonterminal, was not found in name map.) (Residue 193: VAL, Nonterminal, was not found in name map.) (Residue 194: ALA, Nonterminal, was not found in name map.) (Residue 195: VAL, Nonterminal, was not found in name map.) (Residue 196: GLY, Nonterminal, was not found in name map.) (Residue 197: PHE, Nonterminal, was not found in name map.) (Residue 198: GLY, Nonterminal, was not found in name map.) (Residue 199: VAL, Nonterminal, was not found in name map.) (Residue 200: SER, Nonterminal, was not found in name map.) (Residue 201: LYS, Nonterminal, was not found in name map.) (Residue 202: ARG, Nonterminal, was not found in name map.) (Residue 203: GLU, Nonterminal, was not found in name map.) (Residue 204: HIS, Nonterminal, was not found in name map.) (Residue 205: VAL, Nonterminal, was not found in name map.) (Residue 206: VAL, Nonterminal, was not found in name map.) (Residue 207: SER, Nonterminal, was not found in name map.) (Residue 208: LEU, Nonterminal, was not found in name map.) (Residue 209: LEU, Nonterminal, was not found in name map.) (Residue 210: LYS, Nonterminal, was not found in name map.) (Residue 211: GLU, Nonterminal, was not found in name map.) (Residue 212: GLY, Nonterminal, was not found in name map.) (Residue 213: ALA, Nonterminal, was not found in name map.) (Residue 214: ASN, Nonterminal, was not found in name map.) (Residue 215: GLY, Nonterminal, was not found in name map.) (Residue 216: VAL, Nonterminal, was not found in name map.) (Residue 217: VAL, Nonterminal, was not found in name map.) (Residue 218: VAL, Nonterminal, was not found in name map.) (Residue 219: GLY, Nonterminal, was not found in name map.) (Residue 220: SER, Nonterminal, was not found in name map.) (Residue 221: ALA, Nonterminal, was not found in name map.) (Residue 222: LEU, Nonterminal, was not found in name map.) (Residue 223: VAL, Nonterminal, was not found in name map.) (Residue 224: LYS, Nonterminal, was not found in name map.) (Residue 225: ILE, Nonterminal, was not found in name map.) (Residue 226: ILE, Nonterminal, was not found in name map.) (Residue 227: GLY, Nonterminal, was not found in name map.) (Residue 228: GLU, Nonterminal, was not found in name map.) (Residue 229: LYS, Nonterminal, was not found in name map.) (Residue 230: GLY, Nonterminal, was not found in name map.) (Residue 231: ARG, Nonterminal, was not found in name map.) (Residue 232: GLU, Nonterminal, was not found in name map.) (Residue 233: ALA, Nonterminal, was not found in name map.) (Residue 234: THR, Nonterminal, was not found in name map.) (Residue 235: GLU, Nonterminal, was not found in name map.) (Residue 236: PHE, Nonterminal, was not found in name map.) (Residue 237: LEU, Nonterminal, was not found in name map.) (Residue 238: LYS, Nonterminal, was not found in name map.) (Residue 239: LYS, Nonterminal, was not found in name map.) (Residue 240: LYS, Nonterminal, was not found in name map.) (Residue 241: VAL, Nonterminal, was not found in name map.) (Residue 242: GLU, Nonterminal, was not found in name map.) (Residue 243: GLU, Nonterminal, was not found in name map.) (Residue 244: LEU, Nonterminal, was not found in name map.) (Residue 245: LEU, Nonterminal, was not found in name map.) (Residue 246: GLY, Nonterminal, was not found in name map.) Mapped residue ILE, term: Terminal/last, seq. number: 247 to: CILE. (Residue 248: 3rg, Terminal/last, was not found in name map.) Unknown residue: 3rg number: 248 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Created a new atom named: HN1 within residue: .R Created a new atom named: HN2 within residue: .R Created a new atom named: HN3 within residue: .R Joining NMET - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - LYS Created a new atom named: HN within residue: .R Joining LYS - GLN Created a new atom named: HN within residue: .R Joining GLN - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - LEU Created a new atom named: HN within residue: .R Joining LEU - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - TYR Created a new atom named: HN within residue: .R Joining TYR - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ILE Created a new atom named: HN within residue: .R Joining ILE - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - PHE Created a new atom named: HN within residue: .R Joining PHE - SER Created a new atom named: HN within residue: .R Joining SER - ASP Created a new atom named: HN within residue: .R Joining ASP - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ILE Created a new atom named: HN within residue: .R Joining ILE - GLN Created a new atom named: HN within residue: .R Joining GLN - GLU Created a new atom named: HN within residue: .R Joining GLU - SER Created a new atom named: HN within residue: .R Joining SER - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - LYS Created a new atom named: HN within residue: .R Joining LYS - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - PHE Created a new atom named: HN within residue: .R Joining PHE - TRP Created a new atom named: HN within residue: .R Joining TRP - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - SER Created a new atom named: HN within residue: .R Joining SER - SER Created a new atom named: HN within residue: .R Joining SER - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - VAL Created a new atom named: HN within residue: .R Joining VAL - LEU Created a new atom named: HN within residue: .R Joining LEU - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - TYR Created a new atom named: HN within residue: .R Joining TYR - TYR Created a new atom named: HN within residue: .R Joining TYR - ASN Created a new atom named: HN within residue: .R Joining ASN - PRO Joining PRO - ILE Created a new atom named: HN within residue: .R Joining ILE - TYR Created a new atom named: HN within residue: .R Joining TYR - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ALA Created a new atom named: HN within residue: .R Joining ALA - SER Created a new atom named: HN within residue: .R Joining SER - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - PRO Joining PRO - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ILE Created a new atom named: HN within residue: .R Joining ILE - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - VAL Created a new atom named: HN within residue: .R Joining VAL - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - ALA Created a new atom named: HN within residue: .R Joining ALA - ALA Created a new atom named: HN within residue: .R Joining ALA - PRO Joining PRO - ASN Created a new atom named: HN within residue: .R Joining ASN - THR Created a new atom named: HN within residue: .R Joining THR - PRO Joining PRO - ASP Created a new atom named: HN within residue: .R Joining ASP - GLU Created a new atom named: HN within residue: .R Joining GLU - ARG Created a new atom named: HN within residue: .R Joining ARG - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ILE Created a new atom named: HN within residue: .R Joining ILE - ASP Created a new atom named: HN within residue: .R Joining ASP - ASP Created a new atom named: HN within residue: .R Joining ASP - MET Created a new atom named: HN within residue: .R Joining MET - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - VAL Created a new atom named: HN within residue: .R Joining VAL - TYR Created a new atom named: HN within residue: .R Joining TYR - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - TYR Created a new atom named: HN within residue: .R Joining TYR - GLY Created a new atom named: HN within residue: .R Joining GLY - THR Created a new atom named: HN within residue: .R Joining THR - THR Created a new atom named: HN within residue: .R Joining THR - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - ILE Created a new atom named: HN within residue: .R Joining ILE - PRO Joining PRO - LYS Created a new atom named: HN within residue: .R Joining LYS - THR Created a new atom named: HN within residue: .R Joining THR - ALA Created a new atom named: HN within residue: .R Joining ALA - TYR Created a new atom named: HN within residue: .R Joining TYR - ASP Created a new atom named: HN within residue: .R Joining ASP - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - ARG Created a new atom named: HN within residue: .R Joining ARG - ARG Created a new atom named: HN within residue: .R Joining ARG - ALA Created a new atom named: HN within residue: .R Joining ALA - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ILE Created a new atom named: HN within residue: .R Joining ILE - CYS Created a new atom named: HN within residue: .R Joining CYS - ARG Created a new atom named: HN within residue: .R Joining ARG - ASN Created a new atom named: HN within residue: .R Joining ASN - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - ALA Created a new atom named: HN within residue: .R Joining ALA - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - PHE Created a new atom named: HN within residue: .R Joining PHE - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LYS Created a new atom named: HN within residue: .R Joining LYS - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - HIE Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Joining HIE - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - SER Created a new atom named: HN within residue: .R Joining SER - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLU Created a new atom named: HN within residue: .R Joining GLU - GLY Created a new atom named: HN within residue: .R Joining GLY - ALA Created a new atom named: HN within residue: .R Joining ALA - ASN Created a new atom named: HN within residue: .R Joining ASN - GLY Created a new atom named: HN within residue: .R Joining GLY - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - VAL Created a new atom named: HN within residue: .R Joining VAL - GLY Created a new atom named: HN within residue: .R Joining GLY - SER Created a new atom named: HN within residue: .R Joining SER - ALA Created a new atom named: HN within residue: .R Joining ALA - LEU Created a new atom named: HN within residue: .R Joining LEU - VAL Created a new atom named: HN within residue: .R Joining VAL - LYS Created a new atom named: HN within residue: .R Joining LYS - ILE Created a new atom named: HN within residue: .R Joining ILE - ILE Created a new atom named: HN within residue: .R Joining ILE - GLY Created a new atom named: HN within residue: .R Joining GLY - GLU Created a new atom named: HN within residue: .R Joining GLU - LYS Created a new atom named: HN within residue: .R Joining LYS - GLY Created a new atom named: HN within residue: .R Joining GLY - ARG Created a new atom named: HN within residue: .R Joining ARG - GLU Created a new atom named: HN within residue: .R Joining GLU - ALA Created a new atom named: HN within residue: .R Joining ALA - THR Created a new atom named: HN within residue: .R Joining THR - GLU Created a new atom named: HN within residue: .R Joining GLU - PHE Created a new atom named: HN within residue: .R Joining PHE - LEU Created a new atom named: HN within residue: .R Joining LEU - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - LYS Created a new atom named: HN within residue: .R Joining LYS - VAL Created a new atom named: HN within residue: .R Joining VAL - GLU Created a new atom named: HN within residue: .R Joining GLU - GLU Created a new atom named: HN within residue: .R Joining GLU - LEU Created a new atom named: HN within residue: .R Joining LEU - LEU Created a new atom named: HN within residue: .R Joining LEU - GLY Created a new atom named: HN within residue: .R Joining GLY - CILE Created a new atom named: HN within residue: .R Creating new UNIT for residue: 3rg sequence: 249 Created a new atom named: C within residue: .R<3rg 249> Created a new atom named: N within residue: .R<3rg 249> Created a new atom named: O within residue: .R<3rg 249> total atoms in file: 2392 Leap added 1806 missing atoms according to residue templates: 1806 H / lone pairs The file contained 247 atoms not in residue templates > charge complex Total unperturbed charge: 3.000000 Total perturbed charge: 3.000000 > addions complex Cl- 3 Using default radius 1.50 for ion Cl- Adding 3 counter ions to "complex" using 1A grid Used default radius 1.50 for 247 atoms Total solute charge: 3.00 Max atom radius: 2.00 Grid extends from solute vdw + 1.50 to 7.50 Box: enclosing: 4.88 -14.39 39.13 66.63 46.20 106.38 sized: 132.88 113.61 167.13 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 0 sec Volume = 2.49% of box, grid points 52169 (no solvent present) Calculating grid charges charges: 4 sec Placed Cl- in complex at (42.88, 29.61, 66.13). Placed Cl- in complex at (43.88, 16.61, 48.13). Placed Cl- in complex at (24.88, 30.61, 88.13). Done adding ions. > solvatebox complex TIP3PBOX 12 (using default radius 1.500000 for C) (using default radius 1.500000 for N) (using default radius 1.500000 for O) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) Solute vdw bounding box: 49.858 48.222 55.393 Total bounding box for atom centers: 73.858 72.222 79.393 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 5 Adding box at: x=0 y=0 z=0 Center of solvent box is: 28.161524, 28.161524, 37.548698 Adding box at: x=0 y=0 z=1 Center of solvent box is: 28.161524, 28.161524, 18.774349 Adding box at: x=0 y=0 z=2 Center of solvent box is: 28.161524, 28.161524, 0.000000 Adding box at: x=0 y=0 z=3 Center of solvent box is: 28.161524, 28.161524, -18.774349 Adding box at: x=0 y=0 z=4 Center of solvent box is: 28.161524, 28.161524, -37.548698 Adding box at: x=0 y=1 z=0 Center of solvent box is: 28.161524, 9.387175, 37.548698 Adding box at: x=0 y=1 z=1 Center of solvent box is: 28.161524, 9.387175, 18.774349 Adding box at: x=0 y=1 z=2 Center of solvent box is: 28.161524, 9.387175, 0.000000 Adding box at: x=0 y=1 z=3 Center of solvent box is: 28.161524, 9.387175, -18.774349 Adding box at: x=0 y=1 z=4 Center of solvent box is: 28.161524, 9.387175, -37.548698 Adding box at: x=0 y=2 z=0 Center of solvent box is: 28.161524, -9.387175, 37.548698 Adding box at: x=0 y=2 z=1 Center of solvent box is: 28.161524, -9.387175, 18.774349 Adding box at: x=0 y=2 z=2 Center of solvent box is: 28.161524, -9.387175, 0.000000 Adding box at: x=0 y=2 z=3 Center of solvent box is: 28.161524, -9.387175, -18.774349 Adding box at: x=0 y=2 z=4 Center of solvent box is: 28.161524, -9.387175, -37.548698 Adding box at: x=0 y=3 z=0 Center of solvent box is: 28.161524, -28.161524, 37.548698 Adding box at: x=0 y=3 z=1 Center of solvent box is: 28.161524, -28.161524, 18.774349 Adding box at: x=0 y=3 z=2 Center of solvent box is: 28.161524, -28.161524, 0.000000 Adding box at: x=0 y=3 z=3 Center of solvent box is: 28.161524, -28.161524, -18.774349 Adding box at: x=0 y=3 z=4 Center of solvent box is: 28.161524, -28.161524, -37.548698 Adding box at: x=1 y=0 z=0 Center of solvent box is: 9.387175, 28.161524, 37.548698 Adding box at: x=1 y=0 z=1 Center of solvent box is: 9.387175, 28.161524, 18.774349 Adding box at: x=1 y=0 z=2 Center of solvent box is: 9.387175, 28.161524, 0.000000 Adding box at: x=1 y=0 z=3 Center of solvent box is: 9.387175, 28.161524, -18.774349 Adding box at: x=1 y=0 z=4 Center of solvent box is: 9.387175, 28.161524, -37.548698 Adding box at: x=1 y=1 z=0 Center of solvent box is: 9.387175, 9.387175, 37.548698 Adding box at: x=1 y=1 z=1 Center of solvent box is: 9.387175, 9.387175, 18.774349 Adding box at: x=1 y=1 z=2 Center of solvent box is: 9.387175, 9.387175, 0.000000 Adding box at: x=1 y=1 z=3 Center of solvent box is: 9.387175, 9.387175, -18.774349 Adding box at: x=1 y=1 z=4 Center of solvent box is: 9.387175, 9.387175, -37.548698 Adding box at: x=1 y=2 z=0 Center of solvent box is: 9.387175, -9.387175, 37.548698 Adding box at: x=1 y=2 z=1 Center of solvent box is: 9.387175, -9.387175, 18.774349 Adding box at: x=1 y=2 z=2 Center of solvent box is: 9.387175, -9.387175, 0.000000 Adding box at: x=1 y=2 z=3 Center of solvent box is: 9.387175, -9.387175, -18.774349 Adding box at: x=1 y=2 z=4 Center of solvent box is: 9.387175, -9.387175, -37.548698 Adding box at: x=1 y=3 z=0 Center of solvent box is: 9.387175, -28.161524, 37.548698 Adding box at: x=1 y=3 z=1 Center of solvent box is: 9.387175, -28.161524, 18.774349 Adding box at: x=1 y=3 z=2 Center of solvent box is: 9.387175, -28.161524, 0.000000 Adding box at: x=1 y=3 z=3 Center of solvent box is: 9.387175, -28.161524, -18.774349 Adding box at: x=1 y=3 z=4 Center of solvent box is: 9.387175, -28.161524, -37.548698 Adding box at: x=2 y=0 z=0 Center of solvent box is: -9.387175, 28.161524, 37.548698 Adding box at: x=2 y=0 z=1 Center of solvent box is: -9.387175, 28.161524, 18.774349 Adding box at: x=2 y=0 z=2 Center of solvent box is: -9.387175, 28.161524, 0.000000 Adding box at: x=2 y=0 z=3 Center of solvent box is: -9.387175, 28.161524, -18.774349 Adding box at: x=2 y=0 z=4 Center of solvent box is: -9.387175, 28.161524, -37.548698 Adding box at: x=2 y=1 z=0 Center of solvent box is: -9.387175, 9.387175, 37.548698 Adding box at: x=2 y=1 z=1 Center of solvent box is: -9.387175, 9.387175, 18.774349 Adding box at: x=2 y=1 z=2 Center of solvent box is: -9.387175, 9.387175, 0.000000 Adding box at: x=2 y=1 z=3 Center of solvent box is: -9.387175, 9.387175, -18.774349 Adding box at: x=2 y=1 z=4 Center of solvent box is: -9.387175, 9.387175, -37.548698 Adding box at: x=2 y=2 z=0 Center of solvent box is: -9.387175, -9.387175, 37.548698 Adding box at: x=2 y=2 z=1 Center of solvent box is: -9.387175, -9.387175, 18.774349 Adding box at: x=2 y=2 z=2 Center of solvent box is: -9.387175, -9.387175, 0.000000 Adding box at: x=2 y=2 z=3 Center of solvent box is: -9.387175, -9.387175, -18.774349 Adding box at: x=2 y=2 z=4 Center of solvent box is: -9.387175, -9.387175, -37.548698 Adding box at: x=2 y=3 z=0 Center of solvent box is: -9.387175, -28.161524, 37.548698 Adding box at: x=2 y=3 z=1 Center of solvent box is: -9.387175, -28.161524, 18.774349 Adding box at: x=2 y=3 z=2 Center of solvent box is: -9.387175, -28.161524, 0.000000 Adding box at: x=2 y=3 z=3 Center of solvent box is: -9.387175, -28.161524, -18.774349 Adding box at: x=2 y=3 z=4 Center of solvent box is: -9.387175, -28.161524, -37.548698 Adding box at: x=3 y=0 z=0 Center of solvent box is: -28.161524, 28.161524, 37.548698 Adding box at: x=3 y=0 z=1 Center of solvent box is: -28.161524, 28.161524, 18.774349 Adding box at: x=3 y=0 z=2 Center of solvent box is: -28.161524, 28.161524, 0.000000 Adding box at: x=3 y=0 z=3 Center of solvent box is: -28.161524, 28.161524, -18.774349 Adding box at: x=3 y=0 z=4 Center of solvent box is: -28.161524, 28.161524, -37.548698 Adding box at: x=3 y=1 z=0 Center of solvent box is: -28.161524, 9.387175, 37.548698 Adding box at: x=3 y=1 z=1 Center of solvent box is: -28.161524, 9.387175, 18.774349 Adding box at: x=3 y=1 z=2 Center of solvent box is: -28.161524, 9.387175, 0.000000 Adding box at: x=3 y=1 z=3 Center of solvent box is: -28.161524, 9.387175, -18.774349 Adding box at: x=3 y=1 z=4 Center of solvent box is: -28.161524, 9.387175, -37.548698 Adding box at: x=3 y=2 z=0 Center of solvent box is: -28.161524, -9.387175, 37.548698 Adding box at: x=3 y=2 z=1 Center of solvent box is: -28.161524, -9.387175, 18.774349 Adding box at: x=3 y=2 z=2 Center of solvent box is: -28.161524, -9.387175, 0.000000 Adding box at: x=3 y=2 z=3 Center of solvent box is: -28.161524, -9.387175, -18.774349 Adding box at: x=3 y=2 z=4 Center of solvent box is: -28.161524, -9.387175, -37.548698 Adding box at: x=3 y=3 z=0 Center of solvent box is: -28.161524, -28.161524, 37.548698 Adding box at: x=3 y=3 z=1 Center of solvent box is: -28.161524, -28.161524, 18.774349 Adding box at: x=3 y=3 z=2 Center of solvent box is: -28.161524, -28.161524, 0.000000 Adding box at: x=3 y=3 z=3 Center of solvent box is: -28.161524, -28.161524, -18.774349 Adding box at: x=3 y=3 z=4 Center of solvent box is: -28.161524, -28.161524, -37.548698 (using default radius 1.500000 for C) (using default radius 1.500000 for N) (using default radius 1.500000 for O) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) Total vdw box size: 77.095 75.345 82.206 angstroms. Volume: 477509.273 A^3 Mass > 235602.860 amu, Density > 0.819 g/cc (type - hence mass - of one or more atoms could not be found) Added 11551 residues. > saveamberparm complex 1geqc.prmtop 1geqc.inpcrd Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. FATAL: Atom .R<3rg 249>.A does not have a type. Failed to generate parameters Parameter file was not saved.