> Speed? Should make no difference at all. Lennard Jones + Coulomb on > point charges. It is rather not for proteins (that is regular Amber) but > for small (organic) ligand molecules.
I stand corrected. I should point out that David really does this for a living. In comparison, I just pretend. :-) So David, I guess I'd go with GAFF first, MMFF94 fall-back, UFF second fall-back. By its nature, UFF should work for essentially any chemistry. As for speed, both Tim and I spent time going through the Open Babel implementations of MMFF94 and UFF to minimize sqrt(), etc. IIRC, this was good for 10-20% improvement. I don't think anyone has really looked at the GAFF implementation. Thanks for the suggestions David! -Geoff ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
