Muslum Ilgu wrote:
Hi again,
I am sorry I fotgot to mention that I will simulate a drug (an
antibiotic) with 23mer RNA molecule. I am potentially using GROMOS as a
force field to.
GROMOS is a relatively poor choice for simulations involving nucleic acids.
CHARMM or AMBER would be a better choice. The parameterization advice still
applies. There are no easy answers. Parameterization may take weeks or months
and is considered an advanced topic. Not to dissuade you from trying, but be
aware that you're in for a long road no matter what you do.
-Justin
Thanks
On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
" Itæ„€ 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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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