On Wednesday 26 November 2003 16:59, Miguel Howard wrote: > It would also be helpful for me to have a little more background > information about 'force fields' ... just so I can start thinking about > where it fits into the architecture.
A force field is a mathematical description of reasonable 3D chemical structures... the has a cost function based on likelyness for angles, torsion, bond length, and often a few more... E.g. if an angle deviates from the ideal for the two bonds, and penalty is given. By minimizing to total penalty for the whole structure, one gets a reasonable guess of the 3D structure of some compound. Thus, a force field can be used to generate 3D coordinates. There are many force fields around, all often aimed at some class of compounds... e.g. some FF's can only work with CHONSP, but not with metals. There are also force fields aimed at proteins, but which are much less accurate for small organic compounds, e.g. analine. Christoph mentioned, some time ago (on the cdk-devel list?) that he would have a 3-month student working with him, a talented person, who would implement a simple force field. I guess the account is for his... Egon ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
