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.
Methods for parameterizing molecules for OPLS-AA are described in fairly
extensive detail in the 2001 OPLS-AA paper cited in the manual. The manual
itself will only tell you how to implement parameters in Gromacs, not how to
derive them.
-Justin
Thank you
With Regards
M. Kavyashree
On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://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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========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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