From owner-chemistry@ccl.net Wed Jun 18 12:09:01 2008
From: "Jose Duarte duarte!=!molgen.mpg.de" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: rmsd calculation
Message-Id: <-37179-080618055742-22347-/sJF2B0kYRkqBwnBe+4mmQ|a|server.ccl.net>
X-Original-From: Jose Duarte <duarte~!~molgen.mpg.de>
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Date: Wed, 18 Jun 2008 11:25:04 +0200
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Sent to CCL by: Jose Duarte [duarte ~ molgen.mpg.de]
maxcluster does a very good job and very fast rmsd calculations. It also 
can do clustering using a few methods. I'm not sure though of the input 
formats, we have used it only with PDB files here.

See http://www.sbg.bio.ic.ac.uk/~maxcluster/index.html

Jose



--

Jose M. Duarte
Max Planck Institue for Molecular Genetics
Berlin


Antje Wolf antje.wolf(-)scai.fraunhofer.de wrote:
> Sent to CCL by: "Antje  Wolf" [antje.wolf]~[scai.fraunhofer.de]
> Hi,
>
> I am looking for a (free) tool for calculating the RMSD between two molecule conformations, preferably a script or command line tool as I want to use it in batch mode.
> It would be great if this tool also includes the possibility to do a clustering.
>
> Perhaps, someone has a good suggestion.
>
> Thanks in advance,
> Antje>
>
>