1. pdb2gmx, editconf and then solvate. <br>2. use trjconv and make a pdb. <br>3. Take 7 water molecules and put them in the top of your original pdb and start again from there.<br><br><br><br><div class="gmail_quote">On 3 June 2010 09:34, NG HUI WEN <span dir="ltr"><<a href="mailto:HuiWen.Ng@nottingham.edu.my">HuiWen.Ng@nottingham.edu.my</a>></span> wrote:<br>
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<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Looks like I’ve got some work to
do. Thanks Mark!</span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span></p>
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<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <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</span></p>
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<br>
----- Original Message -----<br>
From: NG HUI WEN <<a href="mailto:HuiWen.Ng@nottingham.edu.my" target="_blank">HuiWen.Ng@nottingham.edu.my</a>><br>
Date: Thursday, June 3, 2010 18:08<br>
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a></p>
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<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </span>Hi,</p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </span> </p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </span>I’m
a new gromacs user. I have encountered a problem with pdb2gmx where it
automatically renumbers the residues in my pdb file. </p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </span> </p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </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.</p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </span> </p>
<p class="MsoNormal"><span style="background: rgb(245, 248, 240) none repeat scroll 0% 0%; font-size: 10.5pt; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;">> </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.</p>
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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 << </span></p>
</div></div><p><span style="font-size: 10pt;"><a href="http://www.nottingham.edu.my" target="_blank">Email has been scanned for viruses by UNMC
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