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On 2/04/2012 10:19 AM, Acoot Brett wrote:
<blockquote
cite="mid:1333325994.62863.YahooMailNeo@web121806.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div>Dear All,</div>
<div> </div>
<div>I just run a pdb2gmx of a protein, the error message is "</div>
<div><font size="1"><font size="3">Fatal error:</font></font></div>
<div><font size="1"><font size="3">
</font></font></div>
<div><font size="1"><font size="3">Atom CG is used in an
interaction of type atom in the topology</font></font></div>
<div><font size="1"><font size="3">
</font></font></div>
<div><font size="1"><font size="3">database, but an atom of that
name was not found in residue</font></font></div>
<div><font size="1"><font size="3">
</font></font></div>
<div><font size="3">number 5."</font></div>
<div> </div>
<div>According to the sugestion I have tried to find the reason
in "</div>
<div><a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a>"</div>
<div> </div>
<div>But in that part of Document no this error was explained.</div>
<div> </div>
<div>I am looking forward to getting an explaination from you.</div>
<br>
</div>
</blockquote>
<br>
Like it says, look at residue 5 in your .gro and .rtp input files.
They need to match well enough.<br>
<br>
Mark<br>
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