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<p style="margin-bottom: 0in;">Thank you!</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">I changed the residue names in the .pdb
file to LYQ and GLQ</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">LYQ     NZ      1       GLQ     C      
1       0.13        LYQ     GLQ</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o
processed.gro -water tip3p -chainsep interactive -ignh -rtpres</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;"><br></p><p style="margin-bottom: 0in;">Program pdb2gmx, VERSION 4.5.4
</p>
<p style="margin-bottom: 0in;">Source code file: resall.c, line: 581
</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">Fatal error:
</p>
<p style="margin-bottom: 0in;">Residue &#39;LYQ&#39; not found in residue
topology database
</p>
<p style="margin-bottom: 0in;">For more information and tips for
troubleshooting, please check the GROMACS
</p>
<p style="margin-bottom: 0in;">website at
<a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a>
</p>
<p style="margin-bottom: 0in;">-------------------------------------------------------
</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">I checked
<a href="http://www.gromacs.org/Documentation/File_Formats/Topology_File">http://www.gromacs.org/Documentation/File_Formats/Topology_File</a></p>
<p style="margin-bottom: 0in;">But as you see from the previous mail,
I included LYQ and GLQ to the force field. Maybe I missed something?</p>
<div class="gmail_quote"><br></div><br>-- <br><div dir="ltr"><p style="margin-bottom: 0in;">Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov 
</p></div><br>
</div>