[gmx-users] RNA with small molecule

[Justin A. Lemkul]

Muslum Ilgu wrote:
> Hi all,
> 
> I am trying to simulate RNA with a small molecule. However, I could not 
> find any parameter file described for RNA and small molecule. If anyone 
> knows and shares with me, it is appreciated. 
> 

You haven't said what force field you'd like to use, which is an important 
choice.  Don't pick a force field based on whether or not it contains your 
molecules by default.  Most of them won't contain everything, anyway, in which 
case you have to derive the parameters yourself:

http://www.gromacs.org/Documentation/How-tos/Parameterization

Since you haven't even said what the small molecule is (ethanol? a drug? a 
lipid?) then no one here will be able to do much to help you.

-Justin

> Thanks a lot
> Muslum
> -- 
> Muslum ILGU
> PhD Candidate, Nilsen-Hamilton Laboratory
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
> 3228 Mol. Bio. Bldg
> Ames, IA 50011
> office (515) 294-7305
> 
> " It´s not a shame not to know; what is bad is not asking ".
> 

-- 
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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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