Thanks Jason for your suggestions and the information.
I will definitely do so.
Thanks
Jagur
On Thu, Apr 11, 2013 at 7:45 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> AMBER.ambermd.org
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>
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Received on Fri Apr 12 2013 - 08:30:03 PDT
