[gmx-users] Topology for a new ligand

Kavyashree M hmkvsri at gmail.com
Thu Aug 11 17:48:17 CEST 2011

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.

Thank you
With Regards
M. Kavyashree

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
>> http://www.gromacs.org/**Documentation/How-tos/**Parameterization<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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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