[gmx-users] Topology for a new ligand
Mark.Abraham at anu.edu.au
Fri Aug 12 02:05:41 CEST 2011
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.
> 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
> 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 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
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