[gmx-users] partial atomic charges

MARY VARUGHESE maryvjes1985 at yahoo.co.in
Tue Oct 4 11:21:26 CEST 2011

I read the standard advice for parametrization.
Can anyone suggest the ideal force field and QM method( for paramterization using gaussian say, HF, DFT etc) to study the interaction between a protein and a ligand when i am using GROMCAs simulation program.
Thanking you 
--- On Tue, 4/10/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] partial atomic charges
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, 4 October, 2011, 12:06 PM

On 4/10/2011 5:20 PM, MARY VARUGHESE wrote: 


I , am working on interaction between proteins/nucleic acids and ligands. 
On deriving partial atomic charges using gaussian can anyone suggest,
among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to suggest) and why?
I mean to get the partial atomic charges of the ligand which i have to dock to a protein, which charge derivation method is ideal for gromacs.

Your suggestions will be very much helpful.

The standard advice for parametrization can be found here http://www.gromacs.org/Documentation/How-tos/Parameterization


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