[gmx-users] Partial charges QM to GROMACS

nahren manuel meetnahren at yahoo.com
Fri Jul 11 16:03:57 CEST 2008

Dear Dr. Lemkul,
Thanks for the reply.
Yes I am referring to GROMOS forcefield. So how should i treat my partial charges. 
Kindly advice.

--- On Fri, 7/11/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Partial charges QM to GROMACS
To: meetnahren at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, July 11, 2008, 7:25 PM

Quoting nahren manuel <meetnahren at yahoo.com>:

> Dear Gromacs Users,
> 1. I calculated the partial charges of my ligand using QM. Since GROMACS
> ignores the non-polar hydrogen, is it a good approximation to include the
> charges as it is from QM method to my ligand heavy atoms ?.

Gromacs does no such thing!  What you're referring to is the *Gromos* force
field, which is an entirely separate idea.

There are all-atom force fields for use with Gromacs - OPLS, Amber, and even
CHARMM, if you're adventurous :-)  What you need to be concerned with is
whether or not these QM charges and methodology are compatible with your force
field of choice.

> 2.  should i adjust that partial charges , If so how to do the same?

See above.


> regards,
> nahren


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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