Hi again,<div>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.</div><div><br></div><div>Thanks <br><br><div class="gmail_quote">
On Fri, Jan 21, 2011 at 2:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Muslum Ilgu wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
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. <br>
</blockquote>
<br></div>
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:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thanks a lot<br>
Muslum<br>
-- <br>
Muslum ILGU<br>
PhD Candidate, Nilsen-Hamilton Laboratory<br>
Department of Biochemistry, Biophysics and Molecular Biology<br>
Iowa State University<br>
3228 Mol. Bio. Bldg<br>
Ames, IA 50011<br>
office (515) 294-7305<br>
<br></div>
" It愀 not a shame not to know; what is bad is not asking ".<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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