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Hi David, <br>
<br>
Yes indeed, there are multiple ways to get a mol2 files besides
using chimera. You can get it from ZInc, or use openbabel or Marvin
Sketch to generate it, for example. <br>
<br>
The result normally comes back within minutes. Are you sure you
included all hydrogens in the mol2 file? Sometimes the system
detects a problem in your mol2 file, and the webpage following the
submission tells you what happened. Maybe you didn't see that if you
were trying to make the submission non-interactive.<br>
<br>
We did not plan to have a non-interactive version of the server
online for now. But if you need a series of molecules for a given
project, we can certainly generate the topologies for you. Please
get back to me regarding this.<br>
<br>
Cheers, <br>
<br>
Michel<br>
<br>
<br>
<br>
<br>
On 10/12/2010 02:28 PM, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
<blockquote
cite="mid:20101012182832.A009325C83@struktbio205.bmc.uu.se"
type="cite">
<fieldset class="mimeAttachmentHeader"><legend
class="mimeAttachmentName">Part 1.2</legend></fieldset>
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<div class="headerdisplayname" style="display: inline;">Subject:
</div>
Re: [gmx-users] Re: swiss param query</td>
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<div class="headerdisplayname" style="display: inline;">From:
</div>
David van der Spoel <a class="moz-txt-link-rfc2396E" href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a></td>
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<div class="headerdisplayname" style="display: inline;">Date:
</div>
Tue, 12 Oct 2010 19:27:26 +0200</td>
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<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>
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<br>
<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">By the way Michel,
<br>
<br>
your website looks very interesting. I would like to make this
process non-interactive, and can generate a mol2 file from a pdb
file using babel (if the pdb file has H already of course) and
hence skip the chimera step. I just submitted a molecule but
haven't got the result yet, is there an off-line version? Or one
where I can send 200 molecules?
<br>
</div>
</blockquote>
<div class="moz-text-html" lang="x-western">==========================================================
<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>
========================================================== </div>
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