Thanks Justin. It worked perfectly.<br><br>Chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Chandan Choudhury wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello gmx-users<br>
<br>
I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields has a complete parameter for them. While in ffamber, I have the <br>
</blockquote>
<br></div>
This is not true. OPLS can handle isolated amino acids, you just have to manually choose the termini in pdb2gmx (using -ter). Use the "zwitterion" forms of the termini, since in fact, you have a zwitterion.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or there is some way out. If I need to define it, how do I retrive the partial charges.<br>
<br>
Any insight would be very helpful.<br>
Thanks<br>
<br>
Chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
</blockquote>
<br></div>
-- <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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