Thank, that did the trick!!!<div><br><div class="gmail_quote">On Fri, Mar 12, 2010 at 7:00 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Ilya,<br>
<br>
If it is an amino acid, albeit modified, you can make pdb2gmx<br>
recognize it as such by adding it to the file 'aminoacids.dat'. This<br>
file is in the installation directory. You can also copy it to your<br>
working directory and change it there, as it will then take precedence<br>
over the other one. Do mind to increment the number at the top of the<br>
file for every amino acid you add.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Fri, Mar 12, 2010 at 3:56 PM, Joe Joe <<a href="mailto:ilchorny@gmail.com">ilchorny@gmail.com</a>> wrote:<br>
> How do I tell pdb2gmx what the termini are in my molecule. I added a non<br>
> standard amino acid to the ffoplsaa.rtp database but pdb2gmx says "No N- or<br>
> C-terminus found: this chain appears to contain no protein".<br>
> thanks,<br>
> Ilya<br>
><br>
</div></div>> --<br>
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><br>
<br>
<br>
<br>
</div><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
</font><div><div></div><div class="h5">--<br>
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