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4323 lines
106 KiB
4323 lines
106 KiB
2 years ago
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log started: Fri Jun 3 21:58:00 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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> URA = loadmol2 urea_mod.mol2
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Loading Mol2 file: ./urea_mod.mol2
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Reading MOLECULE named URA
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> loadamberparams urea.frcmod
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Loading parameters: ./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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> check URA
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Checking 'URA'....
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Checking parameters for unit 'URA'.
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Checking for bond parameters.
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Checking for angle parameters.
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Unit is OK.
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> saveoff URA URA.lib
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Creating URA.lib
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Saving URA.
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Building topology.
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Building atom parameters.
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> saveamberparm URA URA.parmtop URA.inpcrd
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Checking Unit.
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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 3 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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URA 1
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)
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(no restraints)
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> savepdb URA URA_gaff.pdb
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Writing pdb file: URA_gaff.pdb
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> quit
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Quit
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Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
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log started: Fri Jun 3 22:01:48 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.
|
||
|
|
>> # This file is mostly for use with Antechamber
|
||
|
|
>> #
|
||
|
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>> # load atom type hybridizations
|
||
|
|
>> #
|
||
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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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||
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>> { "o" "O" "sp2" }
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||
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>> { "o2" "O" "sp2" }
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||
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>> { "oh" "O" "sp3" }
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||
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>> { "op" "O" "sp3" }
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||
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>> { "oq" "O" "sp3" }
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||
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>> { "os" "O" "sp3" }
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||
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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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||
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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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||
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>> { "cq" "C" "sp2" }
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||
|
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>> { "cu" "C" "sp2" }
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||
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>> { "cv" "C" "sp2" }
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||
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>> { "cx" "C" "sp2" }
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||
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>> { "cy" "C" "sp2" }
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||
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>> { "cz" "C" "sp2" }
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||
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>> { "n" "N" "sp2" }
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>> { "n1" "N" "sp2" }
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||
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>> { "n2" "N" "sp2" }
|
||
|
|
>> { "n3" "N" "sp3" }
|
||
|
|
>> { "n4" "N" "sp3" }
|
||
|
|
>> { "na" "N" "sp2" }
|
||
|
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>> { "nb" "N" "sp2" }
|
||
|
|
>> { "nc" "N" "sp2" }
|
||
|
|
>> { "nd" "N" "sp2" }
|
||
|
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>> { "ne" "N" "sp2" }
|
||
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>> { "nf" "N" "sp2" }
|
||
|
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>> { "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/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
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Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
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Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:07:31 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:08:27 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:09:59 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:50:42 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:51:03 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Fri Jun 3 22:52:04 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:32:56 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:33:19 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:34:50 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:36:36 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:46:12 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:49:02 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 09:56:26 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:00:11 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:03:58 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:07:20 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:26:10 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:29:56 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:32:47 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:33:46 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:34:06 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:35:56 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:40:37 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:43:29 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 10:44:25 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Sun Jun 5 11:11:57 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|
||
|
|
log started: Mon Jun 6 20:34:34 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: /home/adit/miniconda3/dat/leap/parm/gaff.dat
|
||
|
|
Reading title:
|
||
|
|
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
|
||
|
|
>
|
||
|
|
> URA = loadmol2 urea_mod.mol2
|
||
|
|
Loading Mol2 file: ./urea_mod.mol2
|
||
|
|
Reading MOLECULE named URA
|
||
|
|
> loadamberparams urea.frcmod
|
||
|
|
Loading parameters: ./urea.frcmod
|
||
|
|
Reading force field modification type file (frcmod)
|
||
|
|
Reading title:
|
||
|
|
Remark line goes here
|
||
|
|
> check URA
|
||
|
|
Checking 'URA'....
|
||
|
|
Checking parameters for unit 'URA'.
|
||
|
|
Checking for bond parameters.
|
||
|
|
Checking for angle parameters.
|
||
|
|
Unit is OK.
|
||
|
|
> saveoff URA URA.lib
|
||
|
|
Saving URA.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
> saveamberparm URA URA.parmtop URA.inpcrd
|
||
|
|
Checking Unit.
|
||
|
|
Building topology.
|
||
|
|
Building atom parameters.
|
||
|
|
Building bond parameters.
|
||
|
|
Building angle parameters.
|
||
|
|
Building proper torsion parameters.
|
||
|
|
Building improper torsion parameters.
|
||
|
|
total 3 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
|
||
|
|
|
||
|
|
URA 1
|
||
|
|
)
|
||
|
|
(no restraints)
|
||
|
|
> savepdb URA URA_gaff.pdb
|
||
|
|
Writing pdb file: URA_gaff.pdb
|
||
|
|
> quit
|
||
|
|
Quit
|
||
|
|
|
||
|
|
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
|