log started: Wed Jul 10 18:14:50 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > LIG=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > list LIG gaff > check LIG Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > 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. > saveoff LIG ligand_antechamber.pdb Creating ligand_antechamber.pdb 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 25 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) > quit Quit Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. log started: Wed Jul 10 18:15:40 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > LIG=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > list LIG gaff > check LIG Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff LIG ligand.lib Saving LIG. Building topology. Building atom parameters. > savepdb LIG ligand_antechamber.pdb Writing pdb file: ligand_antechamber.pdb > 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 25 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) > quit Quit Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. log started: Wed Jul 10 18:16:36 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Wed Jul 10 18:16:36 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > complex=loadpdb complex_42_final_2_noH.pdb Loading PDB file: ./complex_42_final_2_noH.pdb (starting new molecule for chain ) Matching PDB residue names to LEaP variables. Mapped residue TRP, term: Terminal/beginning, seq. number: 0 to: NTRP. Mapped residue PRO, term: Terminal/last, seq. number: 250 to: CPRO. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1987 Leap added 1911 missing atoms according to residue templates: 7 Heavy 1904 H / lone pairs > saveAmberParm complex rec_ligand.prmtop rec_ligand.inpcrd Checking Unit. Warning: The unperturbed charge of the unit (-6.001000) is not zero. Note: Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 826 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 CPRO 1 LIG 1 NTRP 1 ) (no restraints) > savepdb complex rec_ligand.pdb Writing pdb file: rec_ligand.pdb Warning: Converting N-terminal residue name to PDB format: NTRP -> TRP Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO > charge complex Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > solvateBox complex TIP3PBOX 10.0 Error: solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox complex TIP3PBOX 10 Error: solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox complex TIP3P BOX 10 Error: solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox complex TIP3PBOX 10.0 Error: solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > solvateBox complex TIP3PBOX 10.0 Solute vdw bounding box: 48.246 52.899 51.490 Total bounding box for atom centers: 68.246 72.899 71.490 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 4 Total vdw box size: 71.546 76.278 74.743 angstroms. Volume: 407905.669 A^3 Total mass 198107.200 amu, Density 0.806 g/cc Added 9443 residues. > charge complex Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > addions complex Na+ 6 Error: addIons: Argument #2 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addIons, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > charge complex Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > source ions94.lib ----- Source: /home/ravi/anaconda3/dat/leap/lib/ions94.lib ----- Source of /home/ravi/anaconda3/dat/leap/lib/ions94.lib done >> !!index array str /home/ravi/anaconda3/bin/teLeap: Fatal Error! Error from the parser: syntax error Exiting LEaP: Errors = 7; Warnings = 3; Notes = 1. log started: Wed Jul 10 18:44:31 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Wed Jul 10 18:44:31 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip4pew Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) log started: Wed Jul 10 18:45:04 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Wed Jul 10 18:45:04 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip4pew Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > complex=loadpdb complex_42_final_2_noH.pdb Loading PDB file: ./complex_42_final_2_noH.pdb (starting new molecule for chain ) Matching PDB residue names to LEaP variables. Mapped residue TRP, term: Terminal/beginning, seq. number: 0 to: NTRP. Mapped residue PRO, term: Terminal/last, seq. number: 250 to: CPRO. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1987 Leap added 1911 missing atoms according to residue templates: 7 Heavy 1904 H / lone pairs > charge complex Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > loadoff ions94.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > solvateBox complex TIP3P 10.0 Error: solvateBox: Argument #2 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox complex TIP3PBOX 10.0 Solute vdw bounding box: 48.246 52.899 51.490 Total bounding box for atom centers: 68.246 72.899 71.490 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 4 Total vdw box size: 71.546 76.278 74.743 angstroms. Volume: 407905.669 A^3 Total mass 198107.200 amu, Density 0.806 g/cc Added 9443 residues. > addions complex Na+ 6 Using default radius 1.50 for ion Na+ Adding 6 counter ions to "complex" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.87 to 8.87 Box: enclosing: -31.73 -34.27 -32.95 31.60 34.24 33.13 sized: 96.27 93.73 95.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.68% of box, grid points 56166 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in complex at (2.17, 9.67, -25.46). (Replacing solvent molecule) Placed Na+ in complex at (13.78, 21.40, 13.96). (Replacing solvent molecule) Placed Na+ in complex at (7.27, -10.54, -16.84). (Replacing solvent molecule) Placed Na+ in complex at (-20.45, 10.76, -3.79). (Replacing solvent molecule) Placed Na+ in complex at (-12.12, 19.96, -19.48). (Replacing solvent molecule) Placed Na+ in complex at (-1.00, 23.88, 7.25). Done adding ions. > charge complex Total unperturbed charge: -0.001000 Total perturbed charge: -0.001000 > saveAmberParm complex rec_lig-box.prmtop rec_lig-box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > saveAmberParm complex rec_lig-box.prmtop rec_lig-box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > quit Quit Exiting LEaP: Errors = 13; Warnings = 2; Notes = 0. log started: Thu Jul 11 07:31:17 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Jul 11 07:31:17 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip4pew Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > com=loadpdb complex_42_final_2_noH.pdb Loading PDB file: ./complex_42_final_2_noH.pdb (starting new molecule for chain ) Matching PDB residue names to LEaP variables. Mapped residue TRP, term: Terminal/beginning, seq. number: 0 to: NTRP. Mapped residue PRO, term: Terminal/last, seq. number: 250 to: CPRO. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1987 Leap added 1911 missing atoms according to residue templates: 7 Heavy 1904 H / lone pairs > saveAmberParm rec_ligand.prmtop rec_ligand.inpcrd Error: saveAmberParm: Improper number of arguments! usage: saveAmberParm > saveAmberParm com rec_ligand.prmtop rec_ligand.inpcrd Checking Unit. Warning: The unperturbed charge of the unit (-6.001000) is not zero. Note: Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 826 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 CPRO 1 LIG 1 NTRP 1 ) (no restraints) > savepdb com rec_ligand.pdb Writing pdb file: rec_ligand.pdb Warning: Converting N-terminal residue name to PDB format: NTRP -> TRP Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > solvateBox complex TIP3PBOX 10.0 Error: solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox comp TIP3PBOX 10.0 Error: solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox comp TIP3PBOX 10.0 Error: solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox com TIP3PBOX 10.0 Solute vdw bounding box: 48.246 52.899 51.490 Total bounding box for atom centers: 68.246 72.899 71.490 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 4 Total vdw box size: 71.546 76.278 74.743 angstroms. Volume: 407905.669 A^3 Total mass 198107.200 amu, Density 0.806 g/cc Added 9443 residues. > charge com Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > loadoff ions94.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > addions Na+6 addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addIons, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > charge com Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > loadoff ions94.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > addions com Na+6 addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addIons, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > charge com Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > addions com Na+ 6 Using default radius 1.50 for ion Na+ Adding 6 counter ions to "com" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.87 to 8.87 Box: enclosing: -31.73 -34.27 -32.95 31.60 34.24 33.13 sized: 96.27 93.73 95.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.68% of box, grid points 56166 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in com at (2.17, 9.67, -25.46). (Replacing solvent molecule) Placed Na+ in com at (13.78, 21.40, 13.96). (Replacing solvent molecule) Placed Na+ in com at (7.27, -10.54, -16.84). (Replacing solvent molecule) Placed Na+ in com at (-20.45, 10.76, -3.79). (Replacing solvent molecule) Placed Na+ in com at (-12.12, 19.96, -19.48). (Replacing solvent molecule) Placed Na+ in com at (-1.00, 23.88, 7.25). Done adding ions. > charge com Total unperturbed charge: -0.001000 Total perturbed charge: -0.001000 > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > list com Error: list: Improper number of arguments! usage: list > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ionsjc_tip4pew Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadAmberParm frcmod.ions1lm_126_tip3p Error: Error from the parser: syntax error > loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadAmberParams frcmod.ions1lm_1264_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_1264_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6-4 set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadAmberParams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) > loadAmberParams frcmod.ions1lm_126_iod_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_iod_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 IOD set) > saveAmberParm com rec_ligand_box.prmtop rec_ligand_box.inpcrd Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > quit Quit Exiting LEaP: Errors = 42; Warnings = 9; Notes = 1. log started: Thu Jul 11 07:54:53 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Jul 11 07:54:53 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > com=loadpdb complex_42_final_2_noH.pdb Loading PDB file: ./complex_42_final_2_noH.pdb (starting new molecule for chain ) Matching PDB residue names to LEaP variables. Mapped residue TRP, term: Terminal/beginning, seq. number: 0 to: NTRP. Mapped residue PRO, term: Terminal/last, seq. number: 250 to: CPRO. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1987 Leap added 1911 missing atoms according to residue templates: 7 Heavy 1904 H / lone pairs > savepdb com see.pdb Writing pdb file: see.pdb Warning: Converting N-terminal residue name to PDB format: NTRP -> TRP Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO > saveAmberParm com see_prmtop see_inpcrd Checking Unit. Warning: The unperturbed charge of the unit (-6.001000) is not zero. Note: Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 826 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 CPRO 1 LIG 1 NTRP 1 ) (no restraints) > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > solvateBox complex TIP3PBOX 10.0 Error: solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > charge complex Error: charge: Argument #1 is type String must be of type: [unit molecule residue atom list] usage: charge > loadoff ions94.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > solvateBox com TIP3PBOX 10.0 Solute vdw bounding box: 48.246 52.899 51.490 Total bounding box for atom centers: 68.246 72.899 71.490 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 4 Total vdw box size: 71.546 76.278 74.743 angstroms. Volume: 407905.669 A^3 Total mass 198107.200 amu, Density 0.806 g/cc Added 9443 residues. > charge com Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > addions com Na+ 6 Using default radius 1.50 for ion Na+ Adding 6 counter ions to "com" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.87 to 8.87 Box: enclosing: -31.73 -34.27 -32.95 31.60 34.24 33.13 sized: 96.27 93.73 95.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.68% of box, grid points 56166 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in com at (2.17, 9.67, -25.46). (Replacing solvent molecule) Placed Na+ in com at (13.78, 21.40, 13.96). (Replacing solvent molecule) Placed Na+ in com at (7.27, -10.54, -16.84). (Replacing solvent molecule) Placed Na+ in com at (-20.45, 10.76, -3.79). (Replacing solvent molecule) Placed Na+ in com at (-12.12, 19.96, -19.48). (Replacing solvent molecule) Placed Na+ in com at (-1.00, 23.88, 7.25). Done adding ions. > charge com Total unperturbed charge: -0.001000 Total perturbed charge: -0.001000 > saveAmberParm see_box.inpcrd see_box.prmtop Error: saveAmberParm: Improper number of arguments! usage: saveAmberParm > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ionsff99_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsff99_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for TIP3P water from Aqvist (adapeted) in parm99.dat > loadamberparams frcmod.ions234lm_iod_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 IOD set) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ions1lm_iod Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_iod Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ions1lm_iod Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_iod Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > loadamberparams frcmod.ions1lm_1264_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_1264_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6-4 set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > loadamberparams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) > loadamberparams frcmod.ions1lm_126_iod_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_iod_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 IOD set) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Jul 11 08:15:17 2019 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 /home/ravi/anaconda3/bin/teLeap: Note. Skipping parm10.dat: already loaded >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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" } >> } Substituting map 0HYP -> HYP for 0HYP -> HYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Jul 11 08:15:20 2019 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 /home/ravi/anaconda3/bin/teLeap: Note. Skipping parm10.dat: already loaded >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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" } >> } Substituting map 0HYP -> HYP for 0HYP -> HYP Substituting map 1HYP -> CHYP for 1HYP -> CHYP Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > saveAmberParm com see_box.inpcrd see_box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > quit Quit Exiting LEaP: Errors = 57; Warnings = 12; Notes = 3. log started: Thu Jul 11 08:16:15 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > LIG=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > list LIG gaff > check LIG Checking 'LIG'.... Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. Unit is OK. > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > saveoff LIG ligand.lib Saving LIG. Building topology. Building atom parameters. > savepdb LIG ligand_antechamber.pdb Writing pdb file: ligand_antechamber.pdb > 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 25 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) > i = createAtom ZN Zn2+ 2.0 > set i element "Zn" > set i position { 0 0 0 } > r = createResidue ZN > add r i > ZN = createUnit ZN > add ZN r > saveOff ZN ./atomic_ions.lib Saving ZN. Building topology. Building atom parameters. > source leaprc.gaff ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.gaff ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Thu Jul 11 08:16:39 2019 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" } >> { "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" } >> { "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" } >> { "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 gaff.dat Loading parameters: /home/ravi/anaconda3/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Thu Jul 11 08:16:39 2019 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/ravi/anaconda3/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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/ravi/anaconda3/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" "HYP" } { 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 > > loadAmberParams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN > loadoff ligand.lib Loading library: ./ligand.lib Loading: LIG > loadAmberParams frcmod.ions234lm_iod_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_iod_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 IOD set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > com=loadpdb complex_42_final_2_noH.pdb Loading PDB file: ./complex_42_final_2_noH.pdb (starting new molecule for chain ) Matching PDB residue names to LEaP variables. Mapped residue TRP, term: Terminal/beginning, seq. number: 0 to: NTRP. Mapped residue PRO, term: Terminal/last, seq. number: 250 to: CPRO. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1987 Leap added 1911 missing atoms according to residue templates: 7 Heavy 1904 H / lone pairs > savepdb com see.pdb Writing pdb file: see.pdb Warning: Converting N-terminal residue name to PDB format: NTRP -> TRP Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO > saveAmberParm com see.prmtop see.inpcrd Checking Unit. Warning: The unperturbed charge of the unit (-6.001000) is not zero. Note: Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 826 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 CPRO 1 LIG 1 NTRP 1 ) (no restraints) > source leaprc.water.tip3p ----- Source: /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/ravi/anaconda3/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: ./atomic_ions.lib Loading: ZN >> loadOff solvents.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 = TP3 >> WAT = TP3 >> loadAmberParams frcmod.tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) >> > > solvateBox complex TIP3PBOX 10.0 Error: solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > solvateBox com TIP3PBOX 10.0 Solute vdw bounding box: 48.246 52.899 51.490 Total bounding box for atom centers: 68.246 72.899 71.490 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 4 y= 4 z= 4 Total vdw box size: 71.546 76.278 74.743 angstroms. Volume: 407905.669 A^3 Total mass 198107.200 amu, Density 0.806 g/cc Added 9443 residues. > charge com Total unperturbed charge: -6.001000 Total perturbed charge: -6.001000 > addions com Na+ 6 Error: addIons: Argument #2 is type String must be of type: [unit] addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addIons, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > loadoff ions94.lib Loading library: /home/ravi/anaconda3/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ > addions com Na+ 6 Using default radius 1.50 for ion Na+ Adding 6 counter ions to "com" using 1A grid Total solute charge: -6.00 Max atom radius: 2.00 Grid extends from solute vdw + 2.87 to 8.87 Box: enclosing: -31.73 -34.27 -32.95 31.60 34.24 33.13 sized: 96.27 93.73 95.05 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.68% of box, grid points 56166 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in com at (2.17, 9.67, -25.46). (Replacing solvent molecule) Placed Na+ in com at (13.78, 21.40, 13.96). (Replacing solvent molecule) Placed Na+ in com at (7.27, -10.54, -16.84). (Replacing solvent molecule) Placed Na+ in com at (-20.45, 10.76, -3.79). (Replacing solvent molecule) Placed Na+ in com at (-12.12, 19.96, -19.48). (Replacing solvent molecule) Placed Na+ in com at (-1.00, 23.88, 7.25). Done adding ions. > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > loadamberparams frcmod.ionsff99_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ionsff99_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for TIP3P water from Aqvist (adapeted) in parm99.dat > loadamberparams frcmod.ions1lm_iod Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_iod Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > loadamberparams frcmod.ions1lm_1264_tip3p Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_1264_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6-4 set) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) > loadamberparams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) > loadamberparams frcmod.ions1lm_126_iod_opc Loading parameters: /home/ravi/anaconda3/dat/leap/parm/frcmod.ions1lm_126_iod_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 IOD set) > saveAmberParm com see-box.inpcrd see-box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > addions com Na+ 0 0.001000 0 1 0 0 Na+ ion required to neutralize. Using default radius 1.50 for ion Na+ Adding 0 counter ions to "com" using 1A grid > charge com Total unperturbed charge: -0.001000 Total perturbed charge: -0.001000 > saveAmberParm com see-box.inpcrd see-box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > setBox vdw com centers Error: setBox: Argument #1 is type String must be of type: [unit] usage: setBox vdw|centers [ clearance | ] > setBox com vdw centers Error: setBox: Argument #3 is type String must be of type: [list number] usage: setBox vdw|centers [ clearance | ] > setBox com vdw centers Error: setBox: Argument #3 is type String must be of type: [list number] usage: setBox vdw|centers [ clearance | ] > setBox com "vdw" removing previous box.. (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) Box dimensions: 71.546420 76.278144 74.743205 > saveAmberParm com see-box.inpcrd see-box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved. > setBox com "vdw" removing previous box.. (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) (using default radius 1.500000 for Na+) Box dimensions: 71.546420 76.278144 74.743205 > saveAmberParm com see-box.inpcrd see-box.prmtop Checking Unit. Building topology. Building atom parameters. Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Error: For atom (.R.A) could not find vdW (or other) parameters for type (IP) Warning: Parameter file was not saved.