<p>Hey :)</p>
<p>You probably want to fit on the protein and calculate the RMSD on the ligand. You may need to specify these groups in an index file.</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br><br><p><font color="#500050">
Nancy wrote:
>
> Hi All,
>
> I need to determine the RMSD of a small molecule cocrystallized ligan...</font></p>
I answered this yesterday:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html</a><br>
<br>
If there's some reason you can't get that to work, then don't simply re-post the same original question. Iterative calls to g_rms are quite straightforward to script.<br>
<br>
-Justin<p><font color="#500050">
> Thank you very much,
> Nancy
>
</font></p>
-- <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> | <a href="tel:%28540%29%20231-9080" target="_blank">(540) 231-9080</a><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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