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A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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CMMDE/examples/larutan/UreaAir/SistemLarutan/leap.log

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log started: Thu Apr 28 23:05:06 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)
>
> loadamberparams /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
Loading parameters: /home/adit/miniconda3/dat/leap/parm/frcmod.ions1lm_iod
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P, SPC/E and TIP4P/EW water models (12-6 IOD set)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: Tl+)
(UNKNOWN ATOM TYPE: Cu+)
(UNKNOWN ATOM TYPE: Ag+)
(UNKNOWN ATOM TYPE: NH4+)
(UNKNOWN ATOM TYPE: HE+)
(UNKNOWN ATOM TYPE: HZ+)
(UNKNOWN ATOM TYPE: H3O+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> loadoff ../urea/URA.lib
Loading library: ../urea/URA.lib
Loading: URA
> loadamberparams ../urea/urea.frcmod
Loading parameters: ../urea/urea.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadoff ../water/water.lib
Loading library: ../water/water.lib
Loading: SLV
> loadamberparams ../water/water.frcmod
Loading parameters: ../water/water.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> SYSTEM = loadpdb system_init.pdb
Loading PDB file: ./system_init.pdb
(starting new molecule for chain B)
Matching PDB residue names to LEaP variables.
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with SLV
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
Starting new chain with URA
total atoms in file: 404
> list
SLV SYSTEM URA gaff
> saveamberparm SYSTEM system.prmtop system.inpcrd
Checking Unit.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) is not integral.
/home/adit/miniconda3/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.013100) is not zero.
/home/adit/miniconda3/bin/teLeap: Note.
Ignoring the error and warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 39 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
SLV 100
URA 13
)
(no restraints)
> savepdb SYSTEM system.pdb
Writing pdb file: system.pdb
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1.