>> The UFF values vary wildly from the ones offered by obenergy using UFF >> forcefield (this doesn't mean they are wrong of course, just want to >> understand why)
There are a couple of intentional differences. At one point, I offered to give Greg a patch, but admit that I never did. 1) The UFF paper offers a unique cosine-based angle term. This allows for octahedral complexes, but has the unfortunate consequence of a minimum of the potential energy at 0 and 360 degrees. I have found this really unsatisfactory, and modified the angle terms to give maxima at 0 and 360 -- otherwise angle terms will frequently fall into each other. I'm not sure how other packages solve this, but I would frequently find optimizations failing. 2) The UFF paper has some typos -- many of these have been corrected by Towhee: http://towhee.sourceforge.net/forcefields/uff.html 3) In order to better handle strange coordination numbers, Open Babel has an empirical correction for the coordination number (e.g., 5-coordinate phosphorus, etc.) There are some other minor points, such that the UFF in Open Babel can be useful for VSEPR demonstrations to students (e.g., empirical terms for 5-coordinate and 7-coordinate species, etc.) Hope that helps, -Geoff ------------------------------------------------------------------------------ RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
