[AMBER] non integer charge in antechamber generated mol2 file

From: Raik Grünberg <raik.gruenberg.gmail.com>
Date: Sat, 4 Aug 2012 20:32:59 -0400

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

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:
(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 Grünberg
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Received on Sat Aug 04 2012 - 18:00:02 PDT
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