[gmx-users] Topology for a new ligand

[Mark Abraham]

On 12/08/2011 1:48 AM, 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.

The link you mentioned, and links from it contain all the 
readily-available information. For ATP, you may well find a validated 
topology in the published literature.

Mark

>
> 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
>         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
>
>     ========================================
>     -- 
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