Re: [AMBER] non integer charge in antechamber generated mol2 file

From: Raik Grünberg <>
Date: Sat, 4 Aug 2012 22:38:18 -0400

In case anyone else is having the same issue, attached is a quick and
dirty fix that scales the charges of a mol2 file to the closest
integer charge. input.mol2 corrected.mol2
By default, the script will grab the first *mol2 file and spit out a
file with the same name but with ".corrected" appended.

I still would like to know though whether this rounding issue is a bug
or a mistake on my end...


On Sat, Aug 4, 2012 at 8:32 PM, Raik Grünberg <> wrote:
> Dear all,
> I have used antechamber and parmchk to create a mol2 and frcmod file
> for a small organic protein ligand with a charge of -1. The original
> coordinates were extracted from the PDB and hydrogens added with
> Chimera.
> I then run:
> antechamber -i in.pdb -fi pdb -o out.mol2 -fo mol2 -c bcc -nc -1&
> followed by:
> parmchk -i *mol2 -f mol2 -o out.frcmod
> All seems to have worked and sqm.out reports a total charge of:
>> Total Mulliken Charge = -1.000
> In reality though, the charges of the mol2 file add up to:
> -0.996001
> (In fact, the charges in the output mol2 are different from the sqm.out.)
> This is enough to make the charge neutralization in tleap fail, i.e.
> one ion is added too little, and the overall charge of the system
> cannot be brought to a clean 0.
> I see the same thing happening on two different machines (Ubuntu 12.04
> 64bit), with a fresh Amber/AmberTools12 compilation (default gnu
> compilers), all patches applied.
> Funny enough, if I generate a mol2 with Chimera (which is using
> antechamber from amber version 11) the charges sum up well and the
> problem doesn't seem to exist. But the resulting charges are quite
> different in detail and I want to stick to Amber 12.
> I guess a workaround will be to write a simple script that scales all
> partial charges to enforce a -1.0000 overall charge. Is there any more
> general solution?
> Thanks a lot in advance,
> Raik
> --
> ___________________________________
> Raik Grünberg
> ___________________________________

Raik Grünberg

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Received on Sat Aug 04 2012 - 20:00:02 PDT
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