It's highly unusual to simulate a single amino acid. I don't exactly know what's your purpose with it, but if you really want to do it, you need to generate those parameters.<br>I know there are web services for generating gromos FF parameters for "unusual" molecules, possibly there are such resources for amber or opls too.<br>
<br><div class="gmail_quote">On Mon, Apr 12, 2010 at 8:36 PM, Chandan Choudhury <span dir="ltr"><<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); 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 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 clear="all"><font color="#888888"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
</font><br>--<br>
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