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298 lines
7.9 KiB
298 lines
7.9 KiB
2 years ago
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log started: Thu Apr 28 23:05:06 2022
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Log file: ./leap.log
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>> #
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>> # ----- leaprc for loading the general Amber Force field.
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>> # This file is mostly for use with Antechamber
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>> #
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>> # load atom type hybridizations
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>> #
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>> addAtomTypes {
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>> { "h1" "H" "sp3" }
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>> { "h2" "H" "sp3" }
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>> { "h3" "H" "sp3" }
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>> { "h4" "H" "sp3" }
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>> { "h5" "H" "sp3" }
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>> { "ha" "H" "sp3" }
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>> { "hc" "H" "sp3" }
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>> { "hn" "H" "sp3" }
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>> { "ho" "H" "sp3" }
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>> { "hp" "H" "sp3" }
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>> { "hs" "H" "sp3" }
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>> { "hw" "H" "sp3" }
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>> { "hx" "H" "sp3" }
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>> { "o" "O" "sp2" }
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>> { "o2" "O" "sp2" }
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>> { "oh" "O" "sp3" }
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>> { "op" "O" "sp3" }
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>> { "oq" "O" "sp3" }
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>> { "os" "O" "sp3" }
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>> { "ow" "O" "sp3" }
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>> { "c" "C" "sp2" }
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>> { "c1" "C" "sp2" }
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>> { "c2" "C" "sp2" }
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>> { "c3" "C" "sp3" }
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>> { "ca" "C" "sp2" }
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>> { "cc" "C" "sp2" }
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>> { "cd" "C" "sp2" }
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>> { "ce" "C" "sp2" }
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>> { "cf" "C" "sp2" }
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>> { "cg" "C" "sp2" }
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>> { "ch" "C" "sp2" }
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>> { "cp" "C" "sp2" }
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>> { "cq" "C" "sp2" }
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>> { "cu" "C" "sp2" }
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>> { "cv" "C" "sp2" }
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>> { "cx" "C" "sp2" }
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>> { "cy" "C" "sp2" }
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>> { "cz" "C" "sp2" }
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>> { "n" "N" "sp2" }
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>> { "n1" "N" "sp2" }
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>> { "n2" "N" "sp2" }
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>> { "n3" "N" "sp3" }
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>> { "n4" "N" "sp3" }
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>> { "na" "N" "sp2" }
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>> { "nb" "N" "sp2" }
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>> { "nc" "N" "sp2" }
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>> { "nd" "N" "sp2" }
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>> { "ne" "N" "sp2" }
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>> { "nf" "N" "sp2" }
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>> { "nh" "N" "sp2" }
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>> { "ni" "N" "sp2" }
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>> { "nj" "N" "sp2" }
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>> { "nk" "N" "sp3" }
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>> { "nl" "N" "sp3" }
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>> { "nm" "N" "sp2" }
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>> { "nn" "N" "sp2" }
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>> { "no" "N" "sp2" }
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>> { "np" "N" "sp3" }
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>> { "nq" "N" "sp3" }
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>> { "s" "S" "sp2" }
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>> { "s2" "S" "sp2" }
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>> { "s3" "S" "sp3" }
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>> { "s4" "S" "sp3" }
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>> { "s6" "S" "sp3" }
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>> { "sh" "S" "sp3" }
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>> { "sp" "S" "sp3" }
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>> { "sq" "S" "sp3" }
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>> { "ss" "S" "sp3" }
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>> { "sx" "S" "sp3" }
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>> { "sy" "S" "sp3" }
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>> { "p2" "P" "sp2" }
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>> { "p3" "P" "sp3" }
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>> { "p4" "P" "sp3" }
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>> { "p5" "P" "sp3" }
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>> { "pb" "P" "sp3" }
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>> { "pc" "P" "sp3" }
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>> { "pd" "P" "sp3" }
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>> { "pe" "P" "sp3" }
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>> { "pf" "P" "sp3" }
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>> { "px" "P" "sp3" }
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>> { "py" "P" "sp3" }
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>> { "f" "F" "sp3" }
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>> { "cl" "Cl" "sp3" }
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>> { "br" "Br" "sp3" }
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>> { "i" "I" "sp3" }
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>> }
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>> #
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>> # Load the general force field parameter set.
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>> #
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>> gaff = loadamberparams gaff.dat
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Loading parameters: /home/adit/miniconda3/dat/leap/parm/gaff.dat
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Reading title:
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AMBER General Force Field for organic molecules (Version 1.81, May 2017)
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>
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> loadamberparams /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
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Loading parameters: /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
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Reading force field modification type file (frcmod)
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Reading title:
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Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set)
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(UNKNOWN ATOM TYPE: Li+)
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(UNKNOWN ATOM TYPE: Na+)
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(UNKNOWN ATOM TYPE: K+)
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(UNKNOWN ATOM TYPE: Rb+)
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(UNKNOWN ATOM TYPE: Cs+)
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(UNKNOWN ATOM TYPE: Tl+)
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(UNKNOWN ATOM TYPE: Cu+)
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(UNKNOWN ATOM TYPE: Ag+)
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(UNKNOWN ATOM TYPE: NH4+)
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(UNKNOWN ATOM TYPE: HE+)
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(UNKNOWN ATOM TYPE: HZ+)
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(UNKNOWN ATOM TYPE: H3O+)
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(UNKNOWN ATOM TYPE: F-)
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(UNKNOWN ATOM TYPE: Cl-)
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(UNKNOWN ATOM TYPE: Br-)
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(UNKNOWN ATOM TYPE: I-)
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> loadoff ../urea/URA.lib
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Loading library: ../urea/URA.lib
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Loading: URA
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> loadamberparams ../urea/urea.frcmod
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Loading parameters: ../urea/urea.frcmod
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Reading force field modification type file (frcmod)
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Reading title:
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Remark line goes here
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> loadoff ../water/water.lib
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Loading library: ../water/water.lib
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Loading: SLV
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> loadamberparams ../water/water.frcmod
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Loading parameters: ../water/water.frcmod
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Reading force field modification type file (frcmod)
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Reading title:
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Remark line goes here
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> SYSTEM = loadpdb system_init.pdb
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Loading PDB file: ./system_init.pdb
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(starting new molecule for chain B)
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Matching PDB residue names to LEaP variables.
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with SLV
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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Starting new chain with URA
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total atoms in file: 404
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> list
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SLV SYSTEM URA gaff
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> saveamberparm SYSTEM system.prmtop system.inpcrd
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Checking Unit.
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/home/adit/miniconda3/bin/teLeap: Warning!
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The unperturbed charge of the unit (-0.013100) is not integral.
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/home/adit/miniconda3/bin/teLeap: Warning!
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The unperturbed charge of the unit (-0.013100) is not zero.
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/home/adit/miniconda3/bin/teLeap: Note.
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Ignoring the error and warning from Unit Checking.
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Building topology.
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Building atom parameters.
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Building bond parameters.
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Building angle parameters.
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Building proper torsion parameters.
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Building improper torsion parameters.
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total 39 improper torsions applied
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Building H-Bond parameters.
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Incorporating Non-Bonded adjustments.
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Not Marking per-residue atom chain types.
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Marking per-residue atom chain types.
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(Residues lacking connect0/connect1 -
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these don't have chain types marked:
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res total affected
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SLV 100
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URA 13
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)
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(no restraints)
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> savepdb SYSTEM system.pdb
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Writing pdb file: system.pdb
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> quit
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Quit
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Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1.
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