log started: Thu Jun 29 00:41:47 2017 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /home/rehan/Downloads/amber16/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.8, Mar 2015) > > loadamberparams frcmod.hem Loading parameters: ./frcmod.hem Reading force field modification type file (frcmod) Reading title: Force field modifcations for all-atom heme Unknown keyword: N.B.: para in parameter file. Perhaps a format error? Unknown keyword: six-coo in parameter file. Perhaps a format error? Unknown keyword: Force fiel in parameter file. Perhaps a format error? Unknown keyword: Univers in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: I modified in parameter file. Perhaps a format error? Unknown keyword: addition o in parameter file. Perhaps a format error? (UNKNOWN ATOM TYPE: FE) (UNKNOWN ATOM TYPE: LO) (UNKNOWN ATOM TYPE: LC) (UNKNOWN ATOM TYPE: NP) > loadamberparams heme.frcmod Loading parameters: ./heme.frcmod Reading force field modification type file (frcmod) Reading title: Force field modifcations for all-atom heme Unknown keyword: N.B.: para in parameter file. Perhaps a format error? Unknown keyword: six-coo in parameter file. Perhaps a format error? Unknown keyword: Force fiel in parameter file. Perhaps a format error? Unknown keyword: Univers in parameter file. Perhaps a format error? Unknown keyword: in parameter file. Perhaps a format error? Unknown keyword: I modified in parameter file. Perhaps a format error? Unknown keyword: addition o in parameter file. Perhaps a format error? (UNKNOWN ATOM TYPE: FE) (UNKNOWN ATOM TYPE: LO) (UNKNOWN ATOM TYPE: LC) (UNKNOWN ATOM TYPE: NP) > loadamberprep heme_all.in Loading Prep file: ./heme_all.in (UNKNOWN ATOM TYPE: FE) (UNKNOWN ATOM TYPE: NP) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: NP) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CB) (UNKNOWN ATOM TYPE: CT) (UNKNOWN ATOM TYPE: CT) (no charges read on atoms lines in Heme residue ALL ATOM, Yves names, Bayly-modified) Loaded UNIT: HEM > list HEM gaff