Hi Justin,<br> Thanks for the info. I know that the topologies are provided in that website. But they have used charmm27 ff and converted it to gromacs format. But I want to use gromos96 45a3 ff. <br>I have another question. Suppose I use those topologies for dopc . And for the sugar part, I use gromos96 45a3. Will it create problem when we combine sugar /dopc system?<br>
Thanks<br>Chanchal<br><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Chanchal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi All,<br>
I am a novice in gromacs. I want to study sugar/membrane interaction and I want to use gromos96 45a3 ff. At first I am planning to simulate dopc bilayer + water. I downloaded the pdb file of dopc from the site <a href="http://www.bioinf.uni-sb.de/RB/" target="_blank">http://www.bioinf.uni-sb.de/RB/</a> . Then I typed pdb2gmx_d -f dopc.pdb and choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not found in residue topology database". How can I fix the error?<br>
</blockquote>
<br></div>
This happens because pdb2gmx is not magic. See here:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database</a><br>
<br>
The website you reference provides suitable topologies for this type of simulation, making pdb2gmx unnecessary.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
Chanchal<br>
<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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