log started: Wed Jun 28 17:51:00 2017 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/rehan/Downloads/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/rehan/Downloads/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/rehan/Downloads/amber16/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /home/rehan/Downloads/amber16/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /home/rehan/Downloads/amber16/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff ----- Source of /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Wed Jun 28 17:51:25 2017 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" } >> { "cz" "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" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "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: /home/rehan/Downloads/amber16/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.8, Mar 2015) > > hem = loadmol2 new.mol2 Loading Mol2 file: ./new.mol2 Reading MOLECULE named hem_h.pdb > list ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHID CHIE CHIP CHIS CHYP CILE CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX GLH GLN GLU GLY HID HIE HIP HIS HYP ILE LEU LYN LYS MET NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL PHE PRO SER THR TRP TYR VAL frcmod14SBgaff hem parm10 > check hem Checking 'hem'.... Warning: Close contact of 1.450054 angstroms between .R.A and .R.A Checking parameters for unit 'hem'. Checking for bond parameters. Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: O.3 - O.3 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Checking for angle parameters. Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.3 - C.ar Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.ar - C.2 - H Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H There are missing parameters. check: Warnings: 1 Unit is OK. > loadamberparams hem.frcmod Loading parameters: ./hem.frcmod Reading force field modification type file (frcmod) Reading title: Force field modifcations for all-atom heme /parametros Dario (UNKNOWN ATOM TYPE: FE) (UNKNOWN ATOM TYPE: FO) (UNKNOWN ATOM TYPE: LO) (UNKNOWN ATOM TYPE: LC) > check hem Checking 'hem'.... Warning: Close contact of 1.450054 angstroms between .R.A and .R.A Checking parameters for unit 'hem'. Checking for bond parameters. Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: O.3 - O.3 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Checking for angle parameters. Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.3 - C.ar Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.ar - C.2 - H Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H There are missing parameters. check: Warnings: 1 Unit is OK. > loadamberparams hem.frcmod Loading parameters: ./hem.frcmod Reading force field modification type file (frcmod) Reading title: Force field modifcations for all-atom heme /parametros Dario (UNKNOWN ATOM TYPE: FE) (UNKNOWN ATOM TYPE: FO) (UNKNOWN ATOM TYPE: LO) (UNKNOWN ATOM TYPE: LC) > check hem Checking 'hem'.... Warning: Close contact of 1.450054 angstroms between .R.A and .R.A Checking parameters for unit 'hem'. Checking for bond parameters. Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - C.3 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.2 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: C.2 - O.co2 Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: N.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.2 Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - C.ar Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.3 - H Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: O.3 - O.3 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.2 - C.2 Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.2 - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - C.ar Could not find bond parameter for: C.ar - N.ar Checking for angle parameters. Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.ar - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.3 - C.3 - C.2 Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.2 - C.2 - C.2 Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.3 - C.3 - C.ar Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.3 - H Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: C.3 - C.2 - O.co2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.2 Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: N.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.ar - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.ar Could not find angle parameter: C.3 - C.2 - C.2 Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.3 - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.2 - C.2 Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - N.ar - C.ar Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: O.co2 - C.2 - O.co2 Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - C.ar Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - C.ar Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.3 - H Could not find angle parameter: C.2 - C.2 - H Could not find angle parameter: C.ar - C.2 - H Could not find angle parameter: C.ar - C.ar - N.ar Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.3 - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: C.ar - C.ar - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.2 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H Could not find angle parameter: H - C.3 - H There are missing parameters. check: Warnings: 1 Unit is OK. > saveoff HEM hem.lib saveOff: Argument #1 is type String must be of type: [unit parameter_set list] usage: saveOff > saveoff hem hem.lib Creating hem.lib Saving hem. Building topology. Building atom parameters. > loadoff hem.lib Loading library: ./hem.lib Loading: hem > complex = loadpdb 1FKO_trunc_sus.pdb Could not open file 1FKO_trunc_sus.pdb: not found > complex = loadpdb hnoxo.pdb Loading PDB file: ./hnoxo.pdb Enter zPdbReadScan from call depth 0. 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: TYR, Nonterminal, was not found in name map.) (Residue 2: GLY, Nonterminal, was not found in name map.) (Residue 3: PHE, Nonterminal, was not found in name map.) (Residue 4: VAL, Nonterminal, was not found in name map.) (Residue 5: ASN, Nonterminal, was not found in name map.) (Residue 6: HIS, Nonterminal, was not found in name map.) (Residue 7: ALA, Nonterminal, was not found in name map.) (Residue 8: LEU, Nonterminal, was not found in name map.) (Residue 9: GLU, Nonterminal, was not found in name map.) (Residue 10: LEU, Nonterminal, was not found in name map.) (Residue 11: LEU, Nonterminal, was not found in name map.) (Residue 12: VAL, Nonterminal, was not found in name map.) (Residue 13: ILE, Nonterminal, was not found in name map.) (Residue 14: ARG, Nonterminal, was not found in name map.) (Residue 15: ASN, Nonterminal, was not found in name map.) (Residue 16: TYR, Nonterminal, was not found in name map.) (Residue 17: GLY, Nonterminal, was not found in name map.) (Residue 18: PRO, Nonterminal, was not found in name map.) (Residue 19: GLU, Nonterminal, was not found in name map.) (Residue 20: VAL, Nonterminal, was not found in name map.) (Residue 21: TRP, Nonterminal, was not found in name map.) (Residue 22: GLU, Nonterminal, was not found in name map.) (Residue 23: ASP, Nonterminal, was not found in name map.) (Residue 24: ILE, Nonterminal, was not found in name map.) (Residue 25: LYS, Nonterminal, was not found in name map.) (Residue 26: LYS, Nonterminal, was not found in name map.) (Residue 27: GLU, Nonterminal, was not found in name map.) (Residue 28: ALA, Nonterminal, was not found in name map.) (Residue 29: GLN, Nonterminal, was not found in name map.) (Residue 30: LEU, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: GLU, Nonterminal, was not found in name map.) (Residue 33: GLU, Nonterminal, was not found in name map.) (Residue 34: GLY, Nonterminal, was not found in name map.) (Residue 35: GLN, Nonterminal, was not found in name map.) (Residue 36: PHE, Nonterminal, was not found in name map.) (Residue 37: LEU, Nonterminal, was not found in name map.) (Residue 38: VAL, Nonterminal, was not found in name map.) (Residue 39: ARG, Nonterminal, was not found in name map.) (Residue 40: ILE, Nonterminal, was not found in name map.) (Residue 41: ILE, Nonterminal, was not found in name map.) (Residue 42: TYR, Nonterminal, was not found in name map.) (Residue 43: ASP, Nonterminal, was not found in name map.) (Residue 44: ASP, Nonterminal, was not found in name map.) (Residue 45: SER, Nonterminal, was not found in name map.) (Residue 46: LYS, Nonterminal, was not found in name map.) (Residue 47: THR, Nonterminal, was not found in name map.) (Residue 48: TYR, Nonterminal, was not found in name map.) (Residue 49: ASP, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: VAL, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: ALA, Nonterminal, was not found in name map.) (Residue 54: ALA, Nonterminal, was not found in name map.) (Residue 55: SER, Nonterminal, was not found in name map.) (Residue 56: LYS, Nonterminal, was not found in name map.) (Residue 57: VAL, Nonterminal, was not found in name map.) (Residue 58: LEU, Nonterminal, was not found in name map.) (Residue 59: ASN, Nonterminal, was not found in name map.) (Residue 60: LEU, Nonterminal, was not found in name map.) (Residue 61: ASN, Nonterminal, was not found in name map.) (Residue 62: ALA, Nonterminal, was not found in name map.) (Residue 63: GLY, Nonterminal, was not found in name map.) (Residue 64: GLU, Nonterminal, was not found in name map.) (Residue 65: ILE, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) (Residue 67: GLN, Nonterminal, was not found in name map.) (Residue 68: MET, Nonterminal, was not found in name map.) (Residue 69: PHE, Nonterminal, was not found in name map.) (Residue 70: GLY, Nonterminal, was not found in name map.) (Residue 71: LYS, Nonterminal, was not found in name map.) (Residue 72: MET, Nonterminal, was not found in name map.) (Residue 73: PHE, Nonterminal, was not found in name map.) (Residue 74: PHE, Nonterminal, was not found in name map.) (Residue 75: VAL, Nonterminal, was not found in name map.) (Residue 76: PHE, Nonterminal, was not found in name map.) (Residue 77: CYS, Nonterminal, was not found in name map.) (Residue 78: GLN, Nonterminal, was not found in name map.) (Residue 79: GLU, Nonterminal, was not found in name map.) (Residue 80: SER, Nonterminal, was not found in name map.) (Residue 81: GLY, Nonterminal, was not found in name map.) (Residue 82: TYR, Nonterminal, was not found in name map.) (Residue 83: ASP, Nonterminal, was not found in name map.) (Residue 84: THR, Nonterminal, was not found in name map.) (Residue 85: ILE, Nonterminal, was not found in name map.) (Residue 86: LEU, Nonterminal, was not found in name map.) (Residue 87: ARG, Nonterminal, was not found in name map.) (Residue 88: VAL, Nonterminal, was not found in name map.) (Residue 89: LEU, Nonterminal, was not found in name map.) (Residue 90: GLY, Nonterminal, was not found in name map.) (Residue 91: SER, Nonterminal, was not found in name map.) (Residue 92: ASN, Nonterminal, was not found in name map.) (Residue 93: VAL, Nonterminal, was not found in name map.) (Residue 94: ARG, Nonterminal, was not found in name map.) (Residue 95: GLU, Nonterminal, was not found in name map.) (Residue 96: PHE, Nonterminal, was not found in name map.) (Residue 97: LEU, Nonterminal, was not found in name map.) (Residue 98: GLN, Nonterminal, was not found in name map.) (Residue 99: ASN, Nonterminal, was not found in name map.) (Residue 100: LEU, Nonterminal, was not found in name map.) (Residue 101: ASP, Nonterminal, was not found in name map.) (Residue 102: ALA, Nonterminal, was not found in name map.) (Residue 103: LEU, Nonterminal, was not found in name map.) (Residue 104: HIS, Nonterminal, was not found in name map.) (Residue 105: ASP, Nonterminal, was not found in name map.) (Residue 106: HIS, Nonterminal, was not found in name map.) (Residue 107: LEU, Nonterminal, was not found in name map.) (Residue 108: ALA, Nonterminal, was not found in name map.) (Residue 109: THR, Nonterminal, was not found in name map.) (Residue 110: ILE, Nonterminal, was not found in name map.) (Residue 111: TYR, Nonterminal, was not found in name map.) (Residue 112: PRO, Nonterminal, was not found in name map.) (Residue 113: GLY, Nonterminal, was not found in name map.) (Residue 114: MET, Nonterminal, was not found in name map.) (Residue 115: ARG, Nonterminal, was not found in name map.) (Residue 116: ALA, Nonterminal, was not found in name map.) (Residue 117: PRO, Nonterminal, was not found in name map.) (Residue 118: SER, Nonterminal, was not found in name map.) (Residue 119: PHE, Nonterminal, was not found in name map.) (Residue 120: ARG, Nonterminal, was not found in name map.) (Residue 121: CYS, Nonterminal, was not found in name map.) (Residue 122: THR, Nonterminal, was not found in name map.) (Residue 123: ASP, Nonterminal, was not found in name map.) (Residue 124: ALA, Nonterminal, was not found in name map.) (Residue 125: GLU, Nonterminal, was not found in name map.) (Residue 126: LYS, Nonterminal, was not found in name map.) (Residue 127: GLY, Nonterminal, was not found in name map.) (Residue 128: LYS, Nonterminal, was not found in name map.) (Residue 129: GLY, Nonterminal, was not found in name map.) (Residue 130: LEU, Nonterminal, was not found in name map.) (Residue 131: ILE, Nonterminal, was not found in name map.) (Residue 132: LEU, Nonterminal, was not found in name map.) (Residue 133: HIS, Nonterminal, was not found in name map.) (Residue 134: TYR, Nonterminal, was not found in name map.) (Residue 135: TYR, Nonterminal, was not found in name map.) (Residue 136: SER, Nonterminal, was not found in name map.) (Residue 137: GLU, Nonterminal, was not found in name map.) (Residue 138: ARG, Nonterminal, was not found in name map.) (Residue 139: GLU, Nonterminal, was not found in name map.) (Residue 140: GLY, Nonterminal, was not found in name map.) (Residue 141: LEU, Nonterminal, was not found in name map.) (Residue 142: GLN, Nonterminal, was not found in name map.) (Residue 143: ASP, Nonterminal, was not found in name map.) (Residue 144: ILE, Nonterminal, was not found in name map.) (Residue 145: VAL, Nonterminal, was not found in name map.) (Residue 146: ILE, Nonterminal, was not found in name map.) (Residue 147: GLY, Nonterminal, was not found in name map.) (Residue 148: ILE, Nonterminal, was not found in name map.) (Residue 149: ILE, Nonterminal, was not found in name map.) (Residue 150: LYS, Nonterminal, was not found in name map.) (Residue 151: THR, Nonterminal, was not found in name map.) (Residue 152: VAL, Nonterminal, was not found in name map.) (Residue 153: ALA, Nonterminal, was not found in name map.) (Residue 154: GLN, Nonterminal, was not found in name map.) (Residue 155: GLN, Nonterminal, was not found in name map.) (Residue 156: ILE, Nonterminal, was not found in name map.) (Residue 157: HIS, Nonterminal, was not found in name map.) (Residue 158: GLY, Nonterminal, was not found in name map.) (Residue 159: THR, Nonterminal, was not found in name map.) (Residue 160: GLU, Nonterminal, was not found in name map.) (Residue 161: ILE, Nonterminal, was not found in name map.) (Residue 162: ASP, Nonterminal, was not found in name map.) (Residue 163: MET, Nonterminal, was not found in name map.) (Residue 164: LYS, Nonterminal, was not found in name map.) (Residue 165: VAL, Nonterminal, was not found in name map.) (Residue 166: ILE, Nonterminal, was not found in name map.) (Residue 167: GLN, Nonterminal, was not found in name map.) (Residue 168: GLN, Nonterminal, was not found in name map.) (Residue 169: ARG, Nonterminal, was not found in name map.) (Residue 170: ASN, Nonterminal, was not found in name map.) (Residue 171: GLU, Nonterminal, was not found in name map.) (Residue 172: GLU, Nonterminal, was not found in name map.) (Residue 173: CYS, Nonterminal, was not found in name map.) (Residue 174: ASP, Nonterminal, was not found in name map.) (Residue 175: HIS, Nonterminal, was not found in name map.) (Residue 176: THR, Nonterminal, was not found in name map.) (Residue 177: GLN, Nonterminal, was not found in name map.) (Residue 178: PHE, Nonterminal, was not found in name map.) (Residue 179: LEU, Nonterminal, was not found in name map.) (Residue 180: ILE, Nonterminal, was not found in name map.) (Residue 181: GLU, Nonterminal, was not found in name map.) (Residue 182: GLU, Nonterminal, was not found in name map.) (Residue 183: LYS, Nonterminal, was not found in name map.) (Residue 184: GLU, Nonterminal, was not found in name map.) Mapped residue SER, term: Terminal/last, seq. number: 185 to: CSER. (Residue 186: HEM, Terminal/last, was not found in name map.) Unknown residue: HEM number: 186 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Joining NMET - TYR Joining TYR - GLY Joining GLY - PHE Joining PHE - VAL Joining VAL - ASN Joining ASN - HIE Joining HIE - ALA Joining ALA - LEU Joining LEU - GLU Joining GLU - LEU Joining LEU - LEU Joining LEU - VAL Joining VAL - ILE Joining ILE - ARG Joining ARG - ASN Joining ASN - TYR Joining TYR - GLY Joining GLY - PRO Joining PRO - GLU Joining GLU - VAL Joining VAL - TRP Joining TRP - GLU Joining GLU - ASP Joining ASP - ILE Joining ILE - LYS Joining LYS - LYS Joining LYS - GLU Joining GLU - ALA Joining ALA - GLN Joining GLN - LEU Joining LEU - ASP Joining ASP - GLU Joining GLU - GLU Joining GLU - GLY Joining GLY - GLN Joining GLN - PHE Joining PHE - LEU Joining LEU - VAL Joining VAL - ARG Joining ARG - ILE Joining ILE - ILE Joining ILE - TYR Joining TYR - ASP Joining ASP - ASP Joining ASP - SER Joining SER - LYS Joining LYS - THR Joining THR - TYR Joining TYR - ASP Joining ASP - LEU Joining LEU - VAL Joining VAL - ALA Joining ALA - ALA Joining ALA - ALA Joining ALA - SER Joining SER - LYS Joining LYS - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - LEU Joining LEU - ASN Joining ASN - ALA Joining ALA - GLY Joining GLY - GLU Joining GLU - ILE Joining ILE - LEU Joining LEU - GLN Joining GLN - MET Joining MET - PHE Joining PHE - GLY Joining GLY - LYS Joining LYS - MET Joining MET - PHE Joining PHE - PHE Joining PHE - VAL Joining VAL - PHE Joining PHE - CYS Joining CYS - GLN Joining GLN - GLU Joining GLU - SER Joining SER - GLY Joining GLY - TYR Joining TYR - ASP Joining ASP - THR Joining THR - ILE Joining ILE - LEU Joining LEU - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - GLY Joining GLY - SER Joining SER - ASN Joining ASN - VAL Joining VAL - ARG Joining ARG - GLU Joining GLU - PHE Joining PHE - LEU Joining LEU - GLN Joining GLN - ASN Joining ASN - LEU Joining LEU - ASP Joining ASP - ALA Joining ALA - LEU Joining LEU - HIE Joining HIE - ASP Joining ASP - HIE Joining HIE - LEU Joining LEU - ALA Joining ALA - THR Joining THR - ILE Joining ILE - TYR Joining TYR - PRO Joining PRO - GLY Joining GLY - MET Joining MET - ARG Joining ARG - ALA Joining ALA - PRO Joining PRO - SER Joining SER - PHE Joining PHE - ARG Joining ARG - CYS Joining CYS - THR Joining THR - ASP Joining ASP - ALA Joining ALA - GLU Joining GLU - LYS Joining LYS - GLY Joining GLY - LYS Joining LYS - GLY Joining GLY - LEU Joining LEU - ILE Joining ILE - LEU Joining LEU - HIE Joining HIE - TYR Joining TYR - TYR Joining TYR - SER Joining SER - GLU Joining GLU - ARG Joining ARG - GLU Joining GLU - GLY Joining GLY - LEU Joining LEU - GLN Joining GLN - ASP Joining ASP - ILE Joining ILE - VAL Joining VAL - ILE Joining ILE - GLY Joining GLY - ILE Joining ILE - ILE Joining ILE - LYS Joining LYS - THR Joining THR - VAL Joining VAL - ALA Joining ALA - GLN Joining GLN - GLN Joining GLN - ILE Joining ILE - HIE Joining HIE - GLY Joining GLY - THR Joining THR - GLU Joining GLU - ILE Joining ILE - ASP Joining ASP - MET Joining MET - LYS Joining LYS - VAL Joining VAL - ILE Joining ILE - GLN Joining GLN - GLN Joining GLN - ARG Joining ARG - ASN Joining ASN - GLU Joining GLU - GLU Joining GLU - CYS Joining CYS - ASP Joining ASP - HIE Joining HIE - THR Joining THR - GLN Joining GLN - PHE Joining PHE - LEU Joining LEU - ILE Joining ILE - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - GLU Joining GLU - CSER Creating new UNIT for residue: HEM sequence: 187 Created a new atom named: CAA within residue: .R Created a new atom named: CAB within residue: .R Created a new atom named: CAC within residue: .R Created a new atom named: CAD within residue: .R Created a new atom named: NA within residue: .R Created a new atom named: CBA within residue: .R Created a new atom named: CBB within residue: .R Created a new atom named: CBC within residue: .R Created a new atom named: CBD within residue: .R Created a new atom named: NB within residue: .R Created a new atom named: CGA within residue: .R Created a new atom named: CGD within residue: .R Created a new atom named: ND within residue: .R Created a new atom named: CHA within residue: .R Created a new atom named: CHB within residue: .R Created a new atom named: CHC within residue: .R Created a new atom named: CHD within residue: .R Created a new atom named: CMA within residue: .R Created a new atom named: CMB within residue: .R Created a new atom named: CMC within residue: .R Created a new atom named: CMD within residue: .R Created a new atom named: C1A within residue: .R Created a new atom named: C1B within residue: .R Created a new atom named: C1C within residue: .R Created a new atom named: C1D within residue: .R Created a new atom named: O01 within residue: .R Created a new atom named: O1A within residue: .R Created a new atom named: O1D within residue: .R Created a new atom named: C2A within residue: .R Created a new atom named: C2B within residue: .R Created a new atom named: C2C within residue: .R Created a new atom named: C2D within residue: .R Created a new atom named: O02 within residue: .R Created a new atom named: O2A within residue: .R Created a new atom named: O2D within residue: .R Created a new atom named: C3A within residue: .R Created a new atom named: C3B within residue: .R Created a new atom named: C3C within residue: .R Created a new atom named: C3D within residue: .R Created a new atom named: C4A within residue: .R Created a new atom named: C4B within residue: .R Created a new atom named: C4C within residue: .R Created a new atom named: C4D within residue: .R Created a new atom named: NC within residue: .R Created a new atom named: FE within residue: .R total atoms in file: 1547 Leap added 1479 missing atoms according to residue templates: 1479 H / lone pairs The file contained 45 atoms not in residue templates > saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -12.000000 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. Failed to generate parameters Parameter file was not saved.