log started: Mon Feb 12 18:34:54 2024 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff19SB 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" } >> { "XC" "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. >> # >> set default cmap on >> parm19 = loadamberparams parm19.dat Loading parameters: /opt/amber22/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /opt/amber22/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino19.lib Loading library: /opt/amber22/dat/leap/lib/amino19.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: /opt/amber22/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: /opt/amber22/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.gaff2 ----- Source: /opt/amber22/dat/leap/cmd/leaprc.gaff2 ----- Source of /opt/amber22/dat/leap/cmd/leaprc.gaff2 done >> logFile leap.log log started: Mon Feb 12 18:35:00 2024 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" } >> { "op" "O" "sp3" } >> { "oq" "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" } >> { "cs" "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" } >> { "n5" "N" "sp3" } >> { "n6" "N" "sp3" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "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 gaff2.dat Loading parameters: /opt/amber22/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.2.20, March 2021) (UNKNOWN ATOM TYPE: c6) > > LIG=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > check LIG Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > saveamberparm LIG ligand.prmtop ligand.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for os-ca-ca-ca atoms are: O1 C3 C2 C7 ** Warning: No sp2 improper torsion term for ca-ca-ca-c atoms are: C5 C7 C6 C8 ** Warning: No sp2 improper torsion term for ca-ca-ca-c atoms are: C2 C6 C7 C9 ** Warning: No sp2 improper torsion term for c-ca-ca-ca atoms are: C9 C11 C10 C12 ** Warning: No sp2 improper torsion term for ca-ca-ca-os atoms are: C10 C13 C11 O4 ** Warning: No sp2 improper torsion term for c-ca-ca-ca atoms are: C8 C10 C12 C15 total 10 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 LIG 1 ) (no restraints) > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff LIG ligand.lib Creating ligand.lib Saving LIG. Building topology. Building atom parameters. > saveamberparm LIG ligand.prmtop ligand.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 16 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 LIG 1 ) (no restraints) > 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 LIG 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 frcmod19SBgaff parm19 > quit Quit Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. log started: Mon Feb 12 18:50:24 2024 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff19SB 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" } >> { "XC" "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. >> # >> set default cmap on >> parm19 = loadamberparams parm19.dat Loading parameters: /opt/amber22/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /opt/amber22/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino19.lib Loading library: /opt/amber22/dat/leap/lib/amino19.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: /opt/amber22/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: /opt/amber22/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.gaff2 ----- Source: /opt/amber22/dat/leap/cmd/leaprc.gaff2 ----- Source of /opt/amber22/dat/leap/cmd/leaprc.gaff2 done >> logFile leap.log log started: Mon Feb 12 18:50:29 2024 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" } >> { "op" "O" "sp3" } >> { "oq" "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" } >> { "cs" "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" } >> { "n5" "N" "sp3" } >> { "n6" "N" "sp3" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "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 gaff2.dat Loading parameters: /opt/amber22/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.2.20, March 2021) (UNKNOWN ATOM TYPE: c6) > > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > MOL=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > ETFD=loadpdb ETFD.pdb Loading PDB file: ./ETFD.pdb Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. Mapped residue ARG, term: Terminal/last, seq. number: 881 to: CARG. total atoms in file: 13470 > saveamberparm ETFD ETFD.prmtop ETFD.inpcrd Checking Unit. Warning: There is a bond of 3.235 angstroms between NE2 and CD2 atoms: ------- .R.A and .R.A Warning: The unperturbed charge of the unit (-0.995999) is not zero. Note: Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 2739 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 CARG 1 LIG 1 NMET 1 ) (no restraints) > source leaprc.water.opc ----- Source: /opt/amber22/dat/leap/cmd/leaprc.water.opc ----- Source of /opt/amber22/dat/leap/cmd/leaprc.water.opc done >> # >> # Load OPC water model and ions for OPC + Li/Merz ion parameters >> # (-1 to +4, 12-6 normal usage set) >> # >> addAtomTypes { >> { "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" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> { "OW" "O" "sp3" } >> { "HW" "H" "sp3" } >> { "EP" "" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /opt/amber22/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /opt/amber22/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: O3P Loading: OP3 Loading: OPC Loading: OPC3BOX Loading: OPC3POLBOX Loading: OPCBOX 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 = OPC >> WAT = OPC >> loadAmberParams frcmod.opc Loading parameters: /opt/amber22/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863-3871) (UNKNOWN ATOM TYPE: EP) >> loadAmberParams frcmod.ionslm_126_opc Loading parameters: /opt/amber22/dat/leap/parm/frcmod.ionslm_126_opc Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of atomic ions for the OPC water model (12-6 set) >> > > list ACE AG AL ALA ARG ASH ASN ASP Ag BA BR Be CA CALA CARG CASN CASP CCYS CCYX CD CE CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL CLEU CLYS CMET CO CPHE CPRO CR CS CSER CTHR CTRP CTYR CU CU1 CVAL CYM CYS CYX Ce Cl- Cr DC4 Dy ETFD EU EU3 Er F FB3 FB3BOX FB4 FB4BOX FE FE2 GD3 GLH GLN GLU GLY H3O+ HE+ HG HID HIE HIP HIS HOH HYP HZ+ Hf ILE IN IOD K K+ LA LEU LI LIG LU LYN LYS MEOHBOX MET MG MN MOL NA NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NH4 NHE NHID NHIE NHIP NHIS NI NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ Nd O3P OP3 OPC OPC3BOX OPC3POLBOX OPCBOX PB PD PHE PL3 POL3BOX PR PRO PT Pu QSPCFWBOX RB Ra SER SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm Sn T4E TB THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP TYR Th Tl Tm U4+ V2+ VAL WAT Y YB2 ZN Zr frcmod19SBgaff parm19 > addIons ETFD Na+ 6 Adding 6 counter ions to "ETFD" using 1A grid Total solute charge: -1.00 Max atom radius: 1.98 Grid extends from solute vdw + 2.81 to 8.79 Box: enclosing: -63.01 -62.27 -66.45 43.45 60.73 68.93 sized: 192.99 193.73 189.55 edge: 256.00 Resolution: 1.00 Angstrom. Tree depth: 8 Volume = 1.37% of box, grid points 230606 (no solvent present) Calculating grid charges Placed Na+ in ETFD at (17.99, 7.73, 16.55). Placed Na+ in ETFD at (-33.01, -5.27, 29.55). Placed Na+ in ETFD at (-12.01, -23.27, 9.55). Placed Na+ in ETFD at (9.99, -6.27, 23.55). Placed Na+ in ETFD at (-5.01, 24.73, 24.55). Placed Na+ in ETFD at (8.99, -31.27, 8.55). Done adding ions. > solvateOct ETFD OPCBOX 10.0 Scaling up box by a factor of 1.493275 to meet diagonal cut criterion Solute vdw bounding box: 91.875 101.272 124.904 Total bounding box for atom centers: 154.769 154.769 154.769 (box expansion for 'iso' is 50.0%) Solvent unit box: 18.865 18.478 19.006 The number of boxes: x= 9 y= 9 z= 9 Volume: 1889801.222 A^3 (oct) Total mass 1044260.878 amu, Density 0.918 g/cc Added 52635 residues. > addIonsRand ETFD Na+ 170 Cl- 170 Adding 340 counter ions to "ETFD". 52295 solvent molecules will remain. 0: Placed Na+ in ETFD at (-8.68, -65.07, -9.07). Placed Cl- in ETFD at (23.03, -16.55, 43.71). 0: Placed Na+ in ETFD at (-54.71, -2.89, 11.85). Placed Cl- in ETFD at (-40.82, -53.00, -33.80). 0: Placed Na+ in ETFD at (19.28, 42.77, -37.02). Placed Cl- in ETFD at (12.65, -40.46, -47.48). 0: Placed Na+ in ETFD at (18.75, -38.05, -47.48). Placed Cl- in ETFD at (-36.25, -52.30, 23.79). 0: Placed Na+ in ETFD at (-27.39, -53.89, -11.91). Placed Cl- in ETFD at (15.86, -25.88, 38.87). 0: Placed Na+ in ETFD at (8.12, -9.65, -33.78). Placed Cl- in ETFD at (33.57, 26.47, -27.75). 0: Placed Na+ in ETFD at (-19.87, -23.47, 33.92). Placed Cl- in ETFD at (-5.78, -3.27, -42.51). 0: Placed Na+ in ETFD at (34.39, 5.09, 43.14). Placed Cl- in ETFD at (24.35, 47.67, -40.93). 0: Placed Na+ in ETFD at (25.59, -46.23, -33.82). Placed Cl- in ETFD at (50.90, 30.26, 22.62). 0: Placed Na+ in ETFD at (-16.48, -47.97, 5.45). Placed Cl- in ETFD at (-45.09, -7.82, 43.25). 0: Placed Na+ in ETFD at (-24.98, -9.43, 38.67). Placed Cl- in ETFD at (36.94, -45.03, 51.46). 0: Placed Na+ in ETFD at (25.59, 19.36, 48.08). Placed Cl- in ETFD at (40.00, 53.18, -31.93). 0: Placed Na+ in ETFD at (14.78, 50.28, 21.40). Placed Cl- in ETFD at (50.94, -24.03, -21.65). 0: Placed Na+ in ETFD at (23.66, 54.77, 34.55). Placed Cl- in ETFD at (-50.51, -9.93, -30.59). 0: Placed Na+ in ETFD at (-15.38, -22.07, 56.06). Placed Cl- in ETFD at (-32.62, 17.07, -61.11). 0: Placed Na+ in ETFD at (35.99, -19.52, 13.49). Placed Cl- in ETFD at (-56.05, -2.89, 34.02). 0: Placed Na+ in ETFD at (46.08, 22.72, -5.32). Placed Cl- in ETFD at (35.77, -46.31, -29.85). 0: Placed Na+ in ETFD at (34.16, -1.85, 26.70). Placed Cl- in ETFD at (25.05, -37.90, -62.94). 0: Placed Na+ in ETFD at (42.55, 43.65, 2.52). Placed Cl- in ETFD at (-8.79, 3.59, -34.61). 0: Placed Na+ in ETFD at (26.86, -27.10, -59.89). Placed Cl- in ETFD at (-40.29, 20.18, 18.41). 0: Placed Na+ in ETFD at (17.90, -9.91, 41.78). Placed Cl- in ETFD at (-12.12, 31.82, -37.62). 0: Placed Na+ in ETFD at (16.85, -19.03, 2.55). Placed Cl- in ETFD at (9.36, -41.51, 16.85). 0: Placed Na+ in ETFD at (-14.92, 7.88, -78.39). Placed Cl- in ETFD at (-29.13, 46.79, 11.74). 0: Placed Na+ in ETFD at (-0.17, -14.47, 70.93). Placed Cl- in ETFD at (50.68, 0.32, 41.04). 0: Placed Na+ in ETFD at (62.23, 9.29, 30.46). Placed Cl- in ETFD at (-60.39, -1.67, -7.20). 0: Placed Na+ in ETFD at (54.44, -7.54, 22.57). Placed Cl- in ETFD at (23.01, 6.87, -28.62). 0: Placed Na+ in ETFD at (-26.31, -43.80, -16.21). Placed Cl- in ETFD at (-20.48, -49.84, -30.34). 0: Placed Na+ in ETFD at (-43.93, 21.02, 53.84). Placed Cl- in ETFD at (3.42, 59.18, 44.25). 0: Placed Na+ in ETFD at (19.45, -31.03, -11.24). Placed Cl- in ETFD at (-35.50, -11.60, -50.35). 0: Placed Na+ in ETFD at (-30.38, -10.11, -60.53). Placed Cl- in ETFD at (-37.17, 24.36, 2.61). 0: Placed Na+ in ETFD at (23.00, 49.86, 32.13). Placed Cl- in ETFD at (39.81, 2.55, 63.28). 0: Placed Na+ in ETFD at (9.79, 18.48, 31.28). Placed Cl- in ETFD at (47.45, -29.26, 16.20). 0: Placed Na+ in ETFD at (-38.45, -5.75, 11.97). Placed Cl- in ETFD at (-44.38, -14.67, -25.90). 0: Placed Na+ in ETFD at (-23.50, -32.74, -26.00). Placed Cl- in ETFD at (16.87, -14.26, 75.70). 0: Placed Na+ in ETFD at (-11.43, 3.21, 53.76). Placed Cl- in ETFD at (35.47, -42.42, -25.98). 0: Placed Na+ in ETFD at (-28.47, -32.78, 41.04). Placed Cl- in ETFD at (12.95, 47.97, -35.92). 0: Placed Na+ in ETFD at (52.00, -21.93, -26.87). Placed Cl- in ETFD at (-46.88, -24.83, -42.53). 0: Placed Na+ in ETFD at (-44.74, 9.07, 48.32). Placed Cl- in ETFD at (-24.47, 14.63, 66.70). 0: Placed Na+ in ETFD at (-14.11, -29.84, 16.84). Placed Cl- in ETFD at (-36.43, -67.01, 5.49). 0: Placed Na+ in ETFD at (29.39, -10.44, 51.94). Placed Cl- in ETFD at (-11.24, -17.85, -31.50). 0: Placed Na+ in ETFD at (27.77, 25.45, -27.15). Placed Cl- in ETFD at (43.02, 63.19, -25.63). 0: Placed Na+ in ETFD at (24.97, -61.12, -49.60). Placed Cl- in ETFD at (-37.70, 42.58, -16.65). 0: Placed Na+ in ETFD at (-55.51, -40.62, 27.71). Placed Cl- in ETFD at (-5.22, 59.93, 20.26). 0: Placed Na+ in ETFD at (-53.10, -46.69, 30.68). Placed Cl- in ETFD at (19.38, -21.95, 58.19). 0: Placed Na+ in ETFD at (-28.24, -47.68, -6.65). Placed Cl- in ETFD at (-2.91, 6.81, -44.48). 0: Placed Na+ in ETFD at (-27.16, 58.32, -37.27). Placed Cl- in ETFD at (61.56, 9.76, -48.76). 0: Placed Na+ in ETFD at (48.63, 22.59, 4.38). Placed Cl- in ETFD at (50.64, 7.17, 48.25). 0: Placed Na+ in ETFD at (-22.16, 61.03, 46.62). Placed Cl- in ETFD at (29.04, 52.05, 15.10). 0: Placed Na+ in ETFD at (47.19, -31.11, 22.96). Placed Cl- in ETFD at (-7.53, -47.62, -40.80). 0: Placed Na+ in ETFD at (54.19, -23.43, -8.92). Placed Cl- in ETFD at (0.07, -3.76, -60.16). 0: Placed Na+ in ETFD at (51.86, 9.24, 12.32). Placed Cl- in ETFD at (18.00, -56.65, 53.78). 0: Placed Na+ in ETFD at (52.64, -25.56, -9.28). Placed Cl- in ETFD at (35.54, 63.03, -14.53). 0: Placed Na+ in ETFD at (34.94, -45.07, -13.57). Placed Cl- in ETFD at (-46.68, 29.19, -1.35). 0: Placed Na+ in ETFD at (41.13, 63.38, -27.69). Placed Cl- in ETFD at (6.06, 16.66, 49.02). 0: Placed Na+ in ETFD at (6.55, -2.68, 75.57). Placed Cl- in ETFD at (23.60, -59.97, 30.65). 0: Placed Na+ in ETFD at (24.09, 4.86, -48.82). Placed Cl- in ETFD at (-1.93, 51.95, -31.86). 0: Placed Na+ in ETFD at (20.58, -51.83, -41.45). Placed Cl- in ETFD at (9.22, 17.43, 48.63). 0: Placed Na+ in ETFD at (-60.52, 0.52, 41.51). Placed Cl- in ETFD at (-16.37, 13.09, -53.64). 0: Placed Na+ in ETFD at (-48.90, 27.22, -43.06). Placed Cl- in ETFD at (-3.59, 20.95, 30.65). 0: Placed Na+ in ETFD at (-30.11, -33.50, 18.12). Placed Cl- in ETFD at (-8.70, 21.86, -16.81). 0: Placed Na+ in ETFD at (-52.47, 12.85, 25.88). Placed Cl- in ETFD at (-13.53, -59.46, 28.78). 0: Placed Na+ in ETFD at (-12.45, 41.24, -54.05). Placed Cl- in ETFD at (40.62, -51.33, -16.70). 0: Placed Na+ in ETFD at (-37.62, -31.41, -42.70). Placed Cl- in ETFD at (-41.35, 4.99, 65.62). 0: Placed Na+ in ETFD at (49.60, 16.93, 39.12). Placed Cl- in ETFD at (11.03, -14.10, -54.67). 0: Placed Na+ in ETFD at (4.89, -41.40, 38.87). Placed Cl- in ETFD at (11.40, 25.34, 43.05). 0: Placed Na+ in ETFD at (24.73, -19.21, -30.05). Placed Cl- in ETFD at (45.32, 1.80, -8.96). 0: Placed Na+ in ETFD at (19.59, -45.24, 51.45). Placed Cl- in ETFD at (33.70, -24.09, 30.64). 0: Placed Na+ in ETFD at (-18.04, -29.43, -54.70). Placed Cl- in ETFD at (19.34, -61.75, 45.08). 0: Placed Na+ in ETFD at (23.13, -54.37, 10.73). Placed Cl- in ETFD at (-38.47, -67.02, -10.49). 0: Placed Na+ in ETFD at (-38.61, -56.13, 33.87). Placed Cl- in ETFD at (52.93, 29.60, -25.72). 0: Placed Na+ in ETFD at (-25.20, 12.48, -39.83). Placed Cl- in ETFD at (5.48, 61.10, 44.58). 0: Placed Na+ in ETFD at (-40.55, 41.42, -11.33). Placed Cl- in ETFD at (-27.26, 12.44, -55.77). 0: Placed Na+ in ETFD at (-61.97, 23.46, -1.60). Placed Cl- in ETFD at (33.61, -38.17, 18.16). 0: Placed Na+ in ETFD at (23.06, -58.65, -19.20). Placed Cl- in ETFD at (-33.02, -38.81, -30.79). 0: Placed Na+ in ETFD at (-7.84, -53.04, 19.28). Placed Cl- in ETFD at (-58.11, 23.98, 44.47). 0: Placed Na+ in ETFD at (53.83, 37.54, -7.36). Placed Cl- in ETFD at (-35.29, 51.04, -29.57). 0: Placed Na+ in ETFD at (52.64, -47.28, -24.83). Placed Cl- in ETFD at (25.18, -47.00, 56.18). 0: Placed Na+ in ETFD at (-31.32, -54.76, 13.84). Placed Cl- in ETFD at (19.99, 13.17, 34.57). 0: Placed Na+ in ETFD at (-17.67, 7.63, -74.11). Placed Cl- in ETFD at (42.64, 16.91, -25.35). 0: Placed Na+ in ETFD at (-54.42, -50.63, 7.96). Placed Cl- in ETFD at (-39.36, -25.08, 27.70). 0: Placed Na+ in ETFD at (14.37, 42.32, -39.86). Placed Cl- in ETFD at (-9.43, 43.98, -43.09). 0: Placed Na+ in ETFD at (-19.35, 16.96, 3.42). Placed Cl- in ETFD at (-28.17, 0.55, 33.40). 0: Placed Na+ in ETFD at (19.46, -17.67, 32.37). Placed Cl- in ETFD at (-20.37, 20.54, -36.62). 0: Placed Na+ in ETFD at (2.12, 11.25, -63.59). Placed Cl- in ETFD at (-20.69, 45.58, 61.22). 0: Placed Na+ in ETFD at (49.98, -48.28, -40.07). Placed Cl- in ETFD at (-45.22, 47.00, 44.03). 0: Placed Na+ in ETFD at (26.36, -14.27, 51.19). Placed Cl- in ETFD at (-29.13, 56.62, 41.48). 0: Placed Na+ in ETFD at (59.90, 26.37, -10.21). Placed Cl- in ETFD at (25.12, -18.24, -11.71). 0: Placed Na+ in ETFD at (-52.85, -23.42, -19.16). Placed Cl- in ETFD at (-13.98, -42.44, -29.30). 0: Placed Na+ in ETFD at (56.91, -9.96, -33.41). Placed Cl- in ETFD at (-7.90, 46.33, -17.56). 0: Placed Na+ in ETFD at (-50.47, 14.68, -26.96). Placed Cl- in ETFD at (3.80, 18.98, -64.83). 0: Placed Na+ in ETFD at (27.93, -28.39, 1.95). Placed Cl- in ETFD at (61.07, 7.96, 22.74). 0: Placed Na+ in ETFD at (7.47, 24.73, -49.31). Placed Cl- in ETFD at (-14.31, 43.74, -41.16). 0: Placed Na+ in ETFD at (4.22, 60.47, -41.35). Placed Cl- in ETFD at (23.15, -42.72, 51.03). 0: Placed Na+ in ETFD at (-25.46, -59.67, -5.25). Placed Cl- in ETFD at (-7.92, -22.82, -18.62). 0: Placed Na+ in ETFD at (38.62, -29.23, 43.17). Placed Cl- in ETFD at (-6.75, 67.02, 38.19). 0: Placed Na+ in ETFD at (-4.15, 33.66, 14.50). Placed Cl- in ETFD at (-45.91, -41.28, 18.75). 0: Placed Na+ in ETFD at (62.99, -14.35, 7.68). Placed Cl- in ETFD at (-9.13, -17.80, 52.83). 0: Placed Na+ in ETFD at (21.94, 17.04, 50.56). Placed Cl- in ETFD at (54.58, 28.49, 4.33). 0: Placed Na+ in ETFD at (-56.20, 45.46, 36.97). Placed Cl- in ETFD at (32.25, -17.04, 58.79). 0: Placed Na+ in ETFD at (23.33, 71.61, -10.27). Placed Cl- in ETFD at (14.49, -9.87, -36.26). 0: Placed Na+ in ETFD at (51.79, -16.22, 30.27). Placed Cl- in ETFD at (-14.08, -21.42, 50.19). 0: Placed Na+ in ETFD at (-55.84, 33.32, 33.90). Placed Cl- in ETFD at (-55.54, -42.22, -27.96). 0: Placed Na+ in ETFD at (-52.13, -24.22, -32.27). Placed Cl- in ETFD at (-32.25, -19.75, 34.37). 0: Placed Na+ in ETFD at (13.64, -20.88, -46.14). Placed Cl- in ETFD at (26.56, 41.40, -40.56). 0: Placed Na+ in ETFD at (7.25, 28.50, -40.89). Placed Cl- in ETFD at (-12.63, -15.54, -32.05). 0: Placed Na+ in ETFD at (11.59, -27.66, -51.11). Placed Cl- in ETFD at (28.11, -11.57, 48.07). 0: Placed Na+ in ETFD at (-24.24, 40.76, 57.75). Placed Cl- in ETFD at (36.07, -55.14, 2.12). 0: Placed Na+ in ETFD at (47.14, -30.24, -23.20). Placed Cl- in ETFD at (42.71, 36.83, 40.15). 0: Placed Na+ in ETFD at (-0.37, 17.04, -38.10). Placed Cl- in ETFD at (16.64, -51.84, 42.69). 0: Placed Na+ in ETFD at (35.24, -41.70, 40.95). Placed Cl- in ETFD at (40.21, -4.82, 32.17). 0: Placed Na+ in ETFD at (-57.64, -46.02, -28.08). Placed Cl- in ETFD at (31.08, -10.31, -9.55). 0: Placed Na+ in ETFD at (-61.44, -0.84, -26.96). Placed Cl- in ETFD at (60.73, -7.84, 24.00). 0: Placed Na+ in ETFD at (-13.40, 7.96, -48.03). Placed Cl- in ETFD at (-47.54, 39.40, 32.46). 0: Placed Na+ in ETFD at (-63.21, 18.17, 20.65). Placed Cl- in ETFD at (32.84, -41.01, 5.22). 0: Placed Na+ in ETFD at (-47.69, -33.36, 1.76). Placed Cl- in ETFD at (14.05, -30.30, 65.37). 0: Placed Na+ in ETFD at (26.73, 2.05, -56.33). Placed Cl- in ETFD at (56.22, -7.72, -57.86). 0: Placed Na+ in ETFD at (22.98, 22.27, 29.81). Placed Cl- in ETFD at (19.61, -45.58, 12.60). 0: Placed Na+ in ETFD at (-62.25, 4.47, -34.51). Placed Cl- in ETFD at (-52.33, -0.52, 20.31). 0: Placed Na+ in ETFD at (10.26, -22.86, -56.92). Placed Cl- in ETFD at (43.99, -0.15, 62.04). 0: Placed Na+ in ETFD at (11.19, -48.98, 18.29). Placed Cl- in ETFD at (-36.43, 22.18, -5.38). 0: Placed Na+ in ETFD at (22.69, 14.96, -26.07). Placed Cl- in ETFD at (-1.98, -53.19, 41.10). 0: Placed Na+ in ETFD at (9.47, -63.29, 41.60). Placed Cl- in ETFD at (-15.29, 59.32, -4.20). 0: Placed Na+ in ETFD at (64.45, -13.60, 18.67). Placed Cl- in ETFD at (-47.08, 12.77, 27.89). 0: Placed Na+ in ETFD at (-58.33, 40.45, 21.92). Placed Cl- in ETFD at (-41.58, 5.15, 39.22). 0: Placed Na+ in ETFD at (42.28, 5.05, 16.85). Placed Cl- in ETFD at (-42.47, 10.40, -28.30). 0: Placed Na+ in ETFD at (-13.90, -19.22, -42.64). Placed Cl- in ETFD at (63.89, 14.61, -11.21). 0: Placed Na+ in ETFD at (23.67, -19.36, -21.00). Placed Cl- in ETFD at (51.79, 37.96, -17.80). 0: Placed Na+ in ETFD at (40.84, 38.08, -36.15). Placed Cl- in ETFD at (-27.25, 5.67, 33.60). 0: Placed Na+ in ETFD at (38.46, 59.90, 4.50). Placed Cl- in ETFD at (49.76, 32.73, 16.49). 0: Placed Na+ in ETFD at (1.19, -4.55, 71.87). Placed Cl- in ETFD at (-37.54, 32.33, -59.82). 0: Placed Na+ in ETFD at (19.45, 26.64, -31.43). Placed Cl- in ETFD at (6.56, 40.00, 29.29). 0: Placed Na+ in ETFD at (-45.21, 31.32, 50.97). Placed Cl- in ETFD at (-24.00, -52.19, 35.56). 0: Placed Na+ in ETFD at (40.34, -48.99, 37.67). Placed Cl- in ETFD at (-17.49, -32.01, -33.06). 0: Placed Na+ in ETFD at (32.16, 52.07, -27.34). Placed Cl- in ETFD at (-44.51, -48.42, 27.16). 0: Placed Na+ in ETFD at (11.75, -55.13, 30.64). Placed Cl- in ETFD at (57.45, 17.97, -32.80). 0: Placed Na+ in ETFD at (-45.88, -42.90, -37.59). Placed Cl- in ETFD at (-29.28, 50.47, 13.45). 0: Placed Na+ in ETFD at (-0.54, 27.84, 25.75). Placed Cl- in ETFD at (-50.51, 30.58, 20.31). 0: Placed Na+ in ETFD at (-54.11, -26.13, 27.88). Placed Cl- in ETFD at (63.08, 2.66, -16.73). 0: Placed Na+ in ETFD at (30.69, 70.77, 11.78). Placed Cl- in ETFD at (11.03, 8.74, -18.43). 0: Placed Na+ in ETFD at (-58.34, -20.91, 10.28). Placed Cl- in ETFD at (-55.55, -17.34, -25.93). 0: Placed Na+ in ETFD at (-35.00, -61.46, 7.13). Placed Cl- in ETFD at (-13.49, 12.58, 70.99). 0: Placed Na+ in ETFD at (38.51, -7.38, 41.18). Placed Cl- in ETFD at (-18.41, 21.74, 54.84). 0: Placed Na+ in ETFD at (63.80, 39.56, 25.67). Placed Cl- in ETFD at (13.18, 53.44, 39.97). 0: Placed Na+ in ETFD at (-41.98, -50.53, -4.66). Placed Cl- in ETFD at (-35.85, -55.91, 10.55). 0: Placed Na+ in ETFD at (39.70, 30.12, -45.00). Placed Cl- in ETFD at (-51.00, 18.72, -53.48). 0: Placed Na+ in ETFD at (46.92, 2.14, 20.01). Placed Cl- in ETFD at (47.79, 24.00, -26.12). 0: Placed Na+ in ETFD at (-26.80, 52.65, 29.97). Placed Cl- in ETFD at (29.80, 64.20, -5.53). 0: Placed Na+ in ETFD at (38.82, -46.14, 9.67). Placed Cl- in ETFD at (46.70, -14.88, 21.40). 0: Placed Na+ in ETFD at (37.01, -12.34, 34.51). Placed Cl- in ETFD at (-66.15, 0.19, 14.92). 0: Placed Na+ in ETFD at (59.71, 21.59, -8.29). Placed Cl- in ETFD at (42.71, -30.27, -47.84). 0: Placed Na+ in ETFD at (56.78, 0.59, -16.74). Placed Cl- in ETFD at (-32.99, 32.02, -8.83). 0: Placed Na+ in ETFD at (42.70, -8.69, 22.71). Placed Cl- in ETFD at (23.06, 26.75, -52.56). 0: Placed Na+ in ETFD at (-0.12, -54.51, -26.75). Placed Cl- in ETFD at (49.47, 4.46, -10.51). 0: Placed Na+ in ETFD at (18.18, 19.76, -19.74). Placed Cl- in ETFD at (21.48, -39.72, -58.97). 0: Placed Na+ in ETFD at (29.83, -40.34, -31.04). Placed Cl- in ETFD at (29.62, -14.21, 43.52). 0: Placed Na+ in ETFD at (63.14, -26.88, 16.04). Placed Cl- in ETFD at (-5.31, -17.56, -30.06). 0: Placed Na+ in ETFD at (-51.61, 21.94, -24.65). Placed Cl- in ETFD at (1.84, 25.25, -62.45). 0: Placed Na+ in ETFD at (-50.87, -19.86, -26.11). Placed Cl- in ETFD at (60.85, 18.17, 1.95). 0: Placed Na+ in ETFD at (-0.75, -55.65, 32.64). Placed Cl- in ETFD at (1.96, 24.15, 58.13). 0: Placed Na+ in ETFD at (20.19, -24.34, -38.45). Placed Cl- in ETFD at (-29.19, 19.39, -46.70). 0: Placed Na+ in ETFD at (23.90, -33.69, -25.20). Placed Cl- in ETFD at (1.64, -66.78, 20.27). 0: Placed Na+ in ETFD at (31.14, -4.25, 55.24). Placed Cl- in ETFD at (-54.18, -14.74, 40.84). 0: Placed Na+ in ETFD at (-4.04, -51.54, -44.72). Placed Cl- in ETFD at (-57.70, -32.56, 37.35). 0: Placed Na+ in ETFD at (-17.46, 57.66, 19.17). Placed Cl- in ETFD at (-15.16, -0.22, 48.43). 0: Placed Na+ in ETFD at (-25.82, -71.81, -21.02). Placed Cl- in ETFD at (14.62, -61.75, -33.82). 0: Placed Na+ in ETFD at (5.48, -44.98, 12.72). Placed Cl- in ETFD at (-22.28, 59.50, 26.27). 0: Placed Na+ in ETFD at (16.88, 49.78, -34.03). Placed Cl- in ETFD at (40.72, -52.72, 39.00). 0: Placed Na+ in ETFD at (-12.04, -42.91, 27.63). Placed Cl- in ETFD at (64.72, 29.83, 5.98). 0: Placed Na+ in ETFD at (33.08, 28.65, -34.80). Placed Cl- in ETFD at (-52.32, -3.43, 55.66). 0: Placed Na+ in ETFD at (-31.50, -7.31, 37.33). Placed Cl- in ETFD at (-63.98, 33.85, 31.28). > saveamberparm ETFD ETFD.prmtop ETFD.inpcrd Checking Unit. Warning: There is a bond of 3.235 angstroms between NE2 and CD2 atoms: ------- .R.A and .R.A Warning: The unperturbed charge of the unit (5.004001) is not zero. Note: Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 2739 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. 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 CARG 1 LIG 1 NMET 1 ) (no restraints) > quit Quit Exiting LEaP: Errors = 0; Warnings = 4; Notes = 2.