<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Mark,</span></div><div><span></span> </div><div><span>I have renumbered the residues. Both 2 chains start from Resis 1. The pdb2gmx still does not work. The fifth residue in the chain A is Val, no CG atom. The fifth residue of chain B is Gly, no CG atom.</span></div><div><span></span> </div><div><span>What is your suggestion?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span><font size="2" face="Arial"></div><div><div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div></div><div> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span
style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 2 April 2012 10:32 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] pdb2gmx error<br> </font></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <br><meta content="off" http-equiv="x-dns-prefetch-control"><div id="yiv2123980515">
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On 2/04/2012 10:26 AM, Acoot Brett wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<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>
</div>
</blockquote>
<br>
I didn't suggest you look at *output* files.<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<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>
</div>
</blockquote>
<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 type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<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>
</div>
<div style="font-family: times new roman, new york, times, serif; font-size: 12pt;">
<div style="font-family: times new roman, new york, times, serif; font-size: 12pt;">
<div dir="ltr"> <font size="2" face="Arial"> <b><span style="font-weight: bold;">From:</span></b> Mark
Abraham <a class="yiv2123980515moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au" rel="nofollow" target="_blank" ymailto="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="yiv2123980515moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="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>
</font> </div>
<br>
<div id="yiv2123980515">
<div> On 2/04/2012 10:19 AM, Acoot Brett wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);">
<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 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>
</div>
</div>
<br>
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<br>
</blockquote>
<br>
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