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On 12/08/2011 1:48 AM, Kavyashree M wrote:
<blockquote
cite="mid:CAPLGqjoD6Mt9eK4Nr70FXJthL9cCZMUgQw0-E5nCQ97NE=nD8w@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
The link you mentioned, and links from it contain all the
readily-available information. For ATP, you may well find a
validated topology in the published literature.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPLGqjoD6Mt9eK4Nr70FXJthL9cCZMUgQw0-E5nCQ97NE=nD8w@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Parameterization"
target="_blank">http://www.gromacs.org/Documentation/How-tos/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>
========================================<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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