From chemistry-request*- at -*ccl.net Tue Jan 20 03:57:42 2004
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Message-ID: <400CEDBE.9010404..at..uni-koeln.de>
Date: Tue, 20 Jan 2004 09:58:38 +0100
From: Christoph Steinbeck <c.steinbeck..at..uni-koeln.de>
Reply-To: c.steinbeck..at..uni-koeln.de
Organization: Cologne University Bioinformatics Center
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To: Joel.Freyss..at..Actelion.Com
CC: chemistry..at..ccl.net, raj kumar <vrs_rajkumarbapu..at..yahoo.com>
Subject: Re: CCL:MM2 ForceField in Java
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Joel, we are doing exactly the same at the moment, as part of our 
student education.
Unfortunately, we are at the same point like you, so it seems we 
duplicated some work.
Our MM2 implementation is based on the MM2 parameter set from the Tinker 
package. I would be delighted to exchange some thoughts or the source 
code. My group, embedded in an international team of developers, 
maintains and develops the Chemistry Development Kit (CDK) [1], 
http://cdk.sourceforge.net. This new MM2 implementation will be part of 
CDK very soon.

Cheers,

Chris

[1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; 
Willighagen, E. The Chemistry Development Kit (CDK): An open-source Java 
library for chemo- and bioinformatics. Journal of Chemical Information 
and Computer Sciences 2003, 43, 493-500.

-- 
Dr. rer. nat. habil. Christoph Steinbeck (c.steinbeck..at..uni-koeln.de)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z|lpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

Joel.Freyss..at..Actelion.Com wrote:

 > Hello,
 >
 > I am trying to implement a MM2 forcefield in Java.
 > I found Tinker to be a great help for that work but I wondered if anybody
 > ever tried to develop something like that in Java and has some hints or
 > resources to help me? I need to find a position close to a global minimum
 > in a very short amount of time and the forcefield needs to be reliable.
 >
 > Right now, I implemented the bond stretching, angle bending, torsion and
 > VDW parameters and I get approximative results in about 2s: CH bonds 
with a
 > length of 1.05 A, using the simulated annealing and then the steepest
 > descent algorithm.
 >
 > Any advise?
 > Thanks
 >
 > Joel