<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title></title>
</head>
<body text="#000000" bgcolor="#ffffff">
Hi Ram,<br>
<br>
Please note that the SwissParam parameters have been tested only
with the charmm force field. But this in principle shouldn't prevent
you from TRYING to use these parameters (which come from the Merck
Molecular Force Field in the first place) with OPLS. <br>
<br>
The error you mention should not happen, because all atomtypes
needed by SwissParam should be defined in the ligand.itp file. Are
you sure that you included the ligand.itp file exactly at the right
place in your topol.top file? It should be done as suggested in the
SwissParam tutorial: <br>
<br>
<a class="moz-txt-link-freetext" href="http://www.swissparam.ch/SwissParam_gromacs_tutorial.html">http://www.swissparam.ch/SwissParam_gromacs_tutorial.html</a><br>
<br>
If you are still encountering problems, please send me your
ligand.itp and topol.top files offline. <br>
<br>
Best regards,<br>
Michel<br>
<br>
On 10/12/2010 11:23 AM, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
<blockquote
cite="mid:20101012152327.A2F7425C83@struktbio205.bmc.uu.se"
type="cite">
<fieldset class="mimeAttachmentHeader"><legend
class="mimeAttachmentName">Part 1.2</legend></fieldset>
<table class="header-part1" width="100%" border="0"
cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td>
<div class="headerdisplayname" style="display: inline;">Subject:
</div>
[gmx-users] swiss param query,</td>
</tr>
<tr>
<td>
<div class="headerdisplayname" style="display: inline;">From:
</div>
ram bio <a class="moz-txt-link-rfc2396E" href="mailto:rmbio861@gmail.com"><rmbio861@gmail.com></a></td>
</tr>
<tr>
<td>
<div class="headerdisplayname" style="display: inline;">Date:
</div>
Tue, 12 Oct 2010 16:32:39 +0200</td>
</tr>
</tbody>
</table>
<table class="header-part2" width="100%" border="0"
cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td>
<div class="headerdisplayname" style="display: inline;">To:
</div>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a></td>
</tr>
</tbody>
</table>
<br>
<div class="moz-text-plain" wrap="true" graphical-quote="true"
style="font-family: -moz-fixed; font-size: 12px;"
lang="x-western">
<pre wrap="">Dear Gromacs Users,
I have generated the topology and parameters files for my ligand
through swiss param site. Now i am trying to run a simulation of
protein ligand complex in POPC bilayer using OPLS force field in
Gromacs, but when I am using the grompp command in gromacs for tpr
generation I am getting an error as follows:
Atomtype C5A not found
Please let me know your suggestions, to correct this error, I have
included ligand.itp in the topology file of the protein.
Thanks,
ram
</pre>
</div>
</blockquote>
==========================================================
<br>
Michel Cuendet, Ph.D
<br>
Molecular Modeling Group
<br>
Swiss Institute of Bioinformatics
<br>
CH-1015 Lausanne
<br>
Switzerland
<br>
<a class="moz-txt-link-freetext"
href="http://lausanne.isb-sib.ch/%7Emcuendet/">http://lausanne.isb-sib.ch/~mcuendet/</a>
<br>
==========================================================
</body>
</html>