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    On 2/04/2012 10:26 AM, Acoot Brett wrote:
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      cite="mid:1333326372.55371.YahooMailNeo@web121804.mail.ne1.yahoo.com"
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        <div><span>Hi Mark,</span></div>
        <div><span></span>&nbsp;</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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    </blockquote>
    <br>
    I didn't suggest you look at *output* files.<br>
    <br>
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        <div>&nbsp;</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>
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        <div><span></span>&nbsp;</div>
        <div><span>I am looking forward to getting your suggestion.</span></div>
        <div><span></span>&nbsp;</div>
        <div><span>Cheers,</span></div>
        <div><span></span>&nbsp;</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">&lt;Mark.Abraham@anu.edu.au&gt;</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">&lt;gmx-users@gromacs.org&gt;</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>
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              <div> On 2/04/2012 10:19 AM, Acoot Brett wrote:
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                    <div>Dear All,</div>
                    <div>&nbsp;</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>&nbsp;&nbsp; </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>&nbsp;</div>
                    <div>But in that part of Document no this error was
                      explained.</div>
                    <div>&nbsp;</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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