[gmx-users] Topology for a new ligand

[Justin A. Lemkul]

Kavyashree M wrote:
> Dear users,
> 
> I was mentioning about OPLSAA force field for ATP
> and other small molecule.  I just wanted to know the
> procedure to be followed and some guidance from
> people who have created topologies for such
> molecules manually. I am going through chapter 5 of
> the manual. But wanted some useful suggestions.
> 

Methods for parameterizing molecules for OPLS-AA are described in fairly 
extensive detail in the 2001 OPLS-AA paper cited in the manual.  The manual 
itself will only tell you how to implement parameters in Gromacs, not how to 
derive them.

-Justin

> Thank you
> With Regards
> M. Kavyashree
> 
> 
> On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Kavyashree M wrote:
> 
>         Dear gromacs users,
> 
>         I wanted to know the steps to be followed
>         in order to generate a topology for a new
>         ligand. I went through the mailing list and
>         http://www.gromacs.org/__Documentation/How-tos/__Parameterization
>         <http://www.gromacs.org/Documentation/How-tos/Parameterization>
>         but was not clear.
> 
> 
>     All force fields are different, and since you haven't said which one
>     you're trying to use there's nothing that anyone can tell you.  Read
>     the primary literature for the force field you want to use and
>     follow the procedure laid out therein.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================