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On 2/04/2012 10:26 AM, Acoot Brett wrote:
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<div><span>Hi Mark,</span></div>
<div><span></span> </div>
<div><span>As for the pdb2gmx is the first step, there is still
no gro file and rtp file produced by this step.</span></div>
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<br>
I didn't suggest you look at *output* files.<br>
<br>
<blockquote
cite="mid:1333326372.55371.YahooMailNeo@web121804.mail.ne1.yahoo.com"
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<div> </div>
<div><span>In addition, in my protein the first residue is Resi
71, which means there is no resi 5 at all.</span></div>
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<br>
The fifth in the sequence, then. Perhaps with a terminal residue.
After all, you haven't told us anything about what you're doing.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1333326372.55371.YahooMailNeo@web121804.mail.ne1.yahoo.com"
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<div><span></span> </div>
<div><span>I am looking forward to getting your suggestion.</span></div>
<div><span></span> </div>
<div><span>Cheers,</span></div>
<div><span></span> </div>
<div><span>Acoot</span></div>
<div><br>
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<div dir="ltr"> <font face="Arial" size="2"> <b><span
style="font-weight: bold;">From:</span></b> Mark
Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Monday, 2 April 2012 10:22 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] pdb2gmx error<br>
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<div> On 2/04/2012 10:19 AM, Acoot Brett wrote:
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new roman, new york, times, serif; font-size: 12pt;
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<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"
rel="nofollow" target="_blank">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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