On Thu, Apr 11, 2013 at 7:18 PM, Jagur Lambix <jagurlambix.gmail.com> wrote:
> Hi All,
>
> Is there any tool to parameterize the ligand molecules in Desmond, just
> like the antechamber in Amber?
>
> I wanted to parameterize the protein-ligand molecule using Desmond, but not
> having information how to do that for the ligand.
>
> Any suggestions will be helpful.
>
The best suggestion I can give is probably to ask in a mailing list
centered around asking questions about Desmond (by definition we are more
experienced with Amber software than -not- Amber software that does what
some Amber program also does).
Most of the people on this list would probably use AmberTools (antechamber)
and build an Amber topology file then convert it for use with Desmond.
You can get information on the Amber website about running the Amber FF in
Desmond: http://ambermd.org/desmond.html
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 11 2013 - 17:00:03 PDT
