Thanks Justin. I haven't find any such tutorial or exact relevant research paper. Find some paper though (<a href="http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html">http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html</a> ), not sure how they have done.<br>
<br><div class="gmail_quote">On Tue, Mar 29, 2011 at 8:51 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>
Monisha Hajra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Friends,<br>
<br>
Need a Gromacs tutorial to find effect of pH on catalytic side. Any help?<br>
</blockquote>
<br></div>
There probably isn't one. If it isn't at <a href="http://www.gromacs.org/Documentation/Tutorials" target="_blank">http://www.gromacs.org/Documentation/Tutorials</a> or you can't find it with Google, then it doesn't exist.<br>
<br>
You'll probably want to look into the ability of pdb2gmx to alter side chain protonation state, and otherwise base your procedures on published literature. You may need to use QM/MM rather than vanilla MD for this type of process, depending on your system and your goals.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Regards<br>
<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>
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