Dear users,<br><br>I was mentioning about OPLSAA force field for ATP <br>and other small molecule. I just wanted to know the<br>procedure to be followed and some guidance from<br>people who have created topologies for such <br>
molecules manually. I am going through chapter 5 of <br>the manual. But wanted some useful suggestions.<br><br>Thank you<br>With Regards<br>M. Kavyashree<br><br><br><div class="gmail_quote">On Thu, Aug 11, 2011 at 5:03 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>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear gromacs users,<br>
<br>
I wanted to know the steps to be followed<br>
in order to generate a topology for a new<br>
ligand. I went through the mailing list and<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/<u></u>Parameterization</a><br>
but was not clear.<br>
<br>
</blockquote>
<br></div>
All force fields are different, and since you haven't said which one you're trying to use there's nothing that anyone can tell you. Read the primary literature for the force field you want to use and follow the procedure laid out therein.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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