On 8/10/12 7:14 AM, Mohammad Hossein Kowsari wrote:
Dear Gromacs workers,
I will decide simulate the system of Hypoxanthine (which is rather similar to
Guanine) in water solvent.
as you know, for this molecule, the force field parameter is not defined in
Gromacs database. at this time, people advice contracting of *.itp file
for new molecule. but How it is possible? How I can prepare input files for
Hypoxanthine molecule or any other new molecules in Gromacs package?
Unless someone else has derived suitable parameters, you have to generate them
yourself:
http://www.gromacs.org/Documentation/How-tos/Parameterization
It is a very time-consuming and difficult process. It may take many weeks or
months to create and validate a viable topology before it can be used for other
simulations.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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