[gmx-users] RNA with small molecule

[Muslum Ilgu]

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.

Thanks

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:
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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