Hi,
I read the standard advice for parametrization.
But,
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
Mary
--- On Tue, 4/10/11, Mark Abraham <[email protected]> wrote:
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] partial atomic charges
To: "Discussion list for GROMACS users" <[email protected]>
Date: Tuesday, 4 October, 2011, 12:06 PM
On 4/10/2011 5:20 PM, MARY VARUGHESE wrote:
Hi,
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
Mark
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