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Hi all,<br>
<br>
For the GROMOS force field there's also the automated topology
builder (ATB) from Alpesh Malde and Alan Mark:<br>
<a class="moz-txt-link-freetext" href="http://compbio.biosci.uq.edu.au/atb/">http://compbio.biosci.uq.edu.au/atb/</a><br>
<br>
Cheers,<br>
René<br>
<pre class="moz-signature" cols="72">=====================================================
René Pool
Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-----
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands
Room P 2.75
E: <a class="moz-txt-link-abbreviated" href="mailto:r.pool@vu.nl">r.pool@vu.nl</a>
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
</pre>
<br>
On 07/31/2011 05:21 PM, Andrej Frolov wrote:
<blockquote cite="mid:4E357309.7010509@mis.mpg.de" type="cite">
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charset=ISO-8859-1">
Hello,<br>
<br>
There are several ways to get the topology + force field for an
arbitrary molecule:<br>
<br>
1. "Maestro + Desmond" programs of the Schrodinger software pack
can assign OPLS-AA force filed. The parameters are stored in the
*.cms file.<br>
2. "FFLD_SERVER" of the Schrodinger software:
$SCHRODINGER/utilities/ffld_server. Also OPLS-AA force filed.<br>
You will need to write a script which converts the output to
Gromacs format.<br>
3. "antechamber" + "tleap" of the AmberTools utilities. It can
assign any kind of Amber force field, like General Amber Force
Field.<br>
See an example:<a moz-do-not-send="true"
href="http://compchemmpi.wikispaces.com/Scripts#GenAmberTop">
http://compchemmpi.wikispaces.com/Scripts#GenAmberTop</a><br>
You could use the "amb2gmx" script to convert the generated
Amber topology to Gromacs format:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://ffamber.cnsm.csulb.edu/ffamber-tools.html">http://ffamber.cnsm.csulb.edu/ffamber-tools.html</a><br>
4. ''PRODRG server'' for the united atom GMX force fields.<br>
5. ''Vega ZZ'' and "Vega" can assign OPLS-AA force field, but not
all atom types, bonds etc. are supported.<br>
6. "MCCCS Towhee'' monte carlo code can assign very many force
fields, but, first, one has to create the so-called basic
connectivity map (which atom is covalently bound to which).<br>
<a moz-do-not-send="true" href="http://towhee.sourceforge.net/">http://towhee.sourceforge.net/</a>
<br>
<br>
Kind regards,<br>
Andrey<br>
<span class="moz-txt-tag">-- <br>
</span>Andrey Frolov <br>
PhD student <br>
Max Planck Institute for Mathematics in the Sciences <br>
(MPI f. Mathematik in den Naturwissenschaften) <br>
Inselstr. 22-26, 04103 Leipzig, Germany <br>
e-mail: <a moz-do-not-send="true"
class="moz-txt-link-abbreviated" href="mailto:frolov@mis.mpg.de">frolov@mis.mpg.de</a>
<br>
web: <a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.mis.mpg.de/scicomp/CompPhysChem/GroupMain.html">http://www.mis.mpg.de/scicomp/CompPhysChem/GroupMain.html</a>
<br>
<br>
<br>
<br>
Dear all,<br>
<blockquote
cite="mid:20110729183026.8287525C97@struktbio205.bmc.uu.se"
type="cite">
<pre wrap=""> Is there any other free tool like PRODRG ? PRODRG server couldn't read
PDB file from user any more. It 's not easy to get a free version asap.
Best
Shiyong
</pre>
</blockquote>
<br>
</blockquote>
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