[gmx-users] partial atomic charges

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 4 13:32:44 CEST 2011

> 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.

I'd say there is no definitive answer to that question.  Each force field has 
strengths and weaknesses and requires a different type of parameterization.


> Thanking you
> Mary
> --- 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:
>>     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
>     -----Inline Attachment Follows-----
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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