Re: [AMBER] charge groups of a ligand

From: Thomas Evangelidis <>
Date: Fri, 2 Dec 2011 21:25:41 +0200

Hi Professor Case,

Here's the whole story [it may remind you something :) ] :

I want to run MD simulations of protein ligand complexes with GROMACS,
using the amber99sb-ildn and GAFF. I have created topology files of my
ligands for GROMACS using the GAFF through the ACPYPE program. However, the
geometries of the ligands looked slightly incorrect (due to a few atom
clashes) after energy minimization, therefore I am currently setting up QM
calculations to compute the partial charges and compare them with those
obtained from GAFF. The software I use for QM (NWChem) has an option to
constrain the net charge of a subset of atoms (moieties) to a certain value
(usually zero). I was refering to these moieties with the term "charge
groups" in my first message. Yet, having looked the topology files
generated with ACPYPE, as well as the amber ff files, I assumed that Amber
ffs and GAFF treat every atom as a separate "charge group". Therefore I
posted a question on the mailing list to make sure that my assumption was

So if I want to use the GAFF with my own partial charges there is no need
to constrain the net charge of subsets of atoms to certain values, the only
requirement is the total charge of the ligand to sum up to an integer value
(zero in my case), right?


On 2 December 2011 18:24, David A Case <> wrote:

> On Fri, Dec 02, 2011, Thomas Evangelidis wrote:
> > I have my ligand coordinates in a .pdb file. What would be the easiest
> way
> > to find out the charge groups (a.k.a. atom groups) of a ligand defined by
> > GAFF?
> Use the antechamber program, with the pdb file as input and a mol2 file as
> output. However, neither Amber nor GAFF have anything called a charge
> group
> or and atom group, so this may not be what you are looking for(?).
> ...dac
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Received on Fri Dec 02 2011 - 11:30:02 PST
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