[gmx-users] RNA with small molecule
ilgu at iastate.edu
Fri Jan 21 22:08:03 CET 2011
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.
On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul <jalemkul at 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:
> 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 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愀 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
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