[gmx-users] Topology for a new ligand
hmkvsri at gmail.com
Thu Aug 11 17:48:17 CEST 2011
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.
On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul <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 | (540) 231-9080
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