log started: Tue Jun 7 16:54:15 2022 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: /opt/conda/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > loadamberparams /opt/conda/dat/leap/parm/frcmod.ions1lm_iod Loading parameters: /opt/conda/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: Li+) (UNKNOWN ATOM TYPE: Na+) (UNKNOWN ATOM TYPE: K+) (UNKNOWN ATOM TYPE: Rb+) (UNKNOWN ATOM TYPE: Cs+) (UNKNOWN ATOM TYPE: Tl+) (UNKNOWN ATOM TYPE: Cu+) (UNKNOWN ATOM TYPE: Ag+) (UNKNOWN ATOM TYPE: NH4+) (UNKNOWN ATOM TYPE: HE+) (UNKNOWN ATOM TYPE: HZ+) (UNKNOWN ATOM TYPE: H3O+) (UNKNOWN ATOM TYPE: F-) (UNKNOWN ATOM TYPE: Cl-) (UNKNOWN ATOM TYPE: Br-) (UNKNOWN ATOM TYPE: I-) > loadoff ../urea/URA.lib Loading library: ../urea/URA.lib Loading: URA > loadamberparams ../urea/urea.frcmod Loading parameters: ../urea/urea.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff ../amoniak/AMK.lib Loading library: ../amoniak/AMK.lib Loading: AMK > loadamberparams ../amoniak/amoniak.frcmod Loading parameters: ../amoniak/amoniak.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff ../air/air.lib Loading library: ../air/air.lib Loading: SLV > loadamberparams ../air/air.frcmod Loading parameters: ../air/air.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > SYSTEM = loadpdb system_init.pdb Loading PDB file: ./system_init.pdb (starting new molecule for chain B) (starting new molecule for chain C) Matching PDB residue names to LEaP variables. Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with SLV Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with URA Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK Starting new chain with AMK total atoms in file: 432 > list AMK SLV SYSTEM URA gaff > saveamberparm SYSTEM system.prmtop system.inpcrd Checking Unit. /opt/conda/bin/teLeap: Warning! The unperturbed charge of the unit (-0.109000) is not integral. /opt/conda/bin/teLeap: Warning! The unperturbed charge of the unit (-0.109000) is not zero. /opt/conda/bin/teLeap: Note. Ignoring the error and warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 27 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 AMK 15 SLV 100 URA 9 ) (no restraints) > savepdb SYSTEM system.pdb Writing pdb file: system.pdb > quit Quit Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1.