[gmx-users] How it possible find detail way for start preparing INPUT files for simulation of Hypoxanthine (aq) solution by Gromacs

[Justin Lemkul]

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

-- 
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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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