Re: [AMBER] generating parameters for methane

From: angad sharma <>
Date: Sat, 20 Jun 2020 10:40:36 +0530

i want to generate parameters for methane, but i am facing some problem

antechamber -i meth.pdb -fi pdb -o meth.mol2 -fo mol2 -c bcc
parmchk2 -i meth.mol2 -f mol2 -o meth.frcmod

source leaprc.gaff
unk = loadmol2 meth.mol2
check unk
saveoff unk meth.lib
till here it is okay for one unit of methane but i put 0.1M methane in the
a box ,and do the following commands then i face the given error.

source leaprc.gaff
loadamberparams meth.frcmod
loadoff meth.lib
a = loadpdb meth.pdb
check a
saveamberparm a a.prmtop a.inpcrd

then i get this error
> check a
Checking 'a'....
ERROR: The unperturbed charge of the unit: -0.082000 is not integral.
WARNING: The unperturbed charge of the unit: -0.082000 is not zero.
Checking parameters for unit 'a'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 1

On Tue, Jun 16, 2020 at 3:07 PM angad sharma <>

> how one can generate parameters for methane in LEAP. I have tried with
> antechamber but still i am getting some errors.
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Received on Fri Jun 19 2020 - 22:30:03 PDT
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