[gmx-users] RNA with small molecule

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 21 21:26:07 CET 2011

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:


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.


> 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 ".


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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