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 ".
--
========================================
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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