[gmx-users] RNA with small molecule

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto: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 <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

========================================