Re: CCL:MM2 ForceField in Java



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