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<p class=MsoNormal><span style='color:#1F497D'>Looks like I’ve got some work to
do. Thanks Mark!<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Thursday, June 03, 2010 4:27 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<br>
----- Original Message -----<br>
From: NG HUI WEN <HuiWen.Ng@nottingham.edu.my><br>
Date: Thursday, June 3, 2010 18:08<br>
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file<br>
To: gmx-users@gromacs.org<o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span>Hi,<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span> <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span>I’m
a new gromacs user. I have encountered a problem with pdb2gmx where it
automatically renumbers the residues in my pdb file. <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span> <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span>For
instance, the first residue in my protein F8 has become F1 – this affects all
the residues in the protein, something I find rather inconvenient.<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span> <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;background:#F5F8F0'>> </span>I’ve
been searching the archive for previous posts which might have a solution to
this but no luck so far. I might have been wrong. Many thanks for your help.<o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
I think you're out of luck. IIRC the facility you want is implemented in the
development version, but not yet released. If you re-renumber by hand, then I
suspect everything will be fine after that. grompp just needs something whose
atom and residue naming and ordering matches the .top... how you produce that
doesn't matter to it.<br>
<br>
Mark << <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><a
href="http://www.nottingham.edu.my">Email has been scanned for viruses by UNMC
email management service</a></span><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>>>
<o:p></o:p></span></p>
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