On 2013-02-04 16:24, David Lonie wrote: > Hi list, > > We're in the process of developing Avogadro 2, and I'm currently adding > an interface to perform the obabel minimize operation on a molecule. > > My question: Is there a heuristic that can be used to select the "best" > forcefield for a given molecule? As I understand it: > > * Ghemical is good for pure organics, say only C, H, O, N, S > * MMFF94 is good for dynamics > * UFF is good for non-organics > > This is mostly inline with the documentation on the avogadro wiki: > > http://avogadro.openmolecules.net/wiki/Tutorials:Force_fields > > My big questions are: > > * Are there cases where MMFF94s should be preferred to Ghemical? > * Is GAFF particularly good at any systems that the others handle poorly? > > Comments, corrections, suggestions are welcome!
I would always prefer a well-defined modern force field based on published work. MMF94 is relatively old so GAFF would be my preferred one for cases that are supported. Is there a publication describing Ghemical? My group provides a database of small molecule topologies that have been tested with GAFF (and OPLS/AA) at http://virtualchemistry.org/. This is still relatively small, but the main point is that this kind of tests are available for the popular force fields. How about support for macromolecules? > > Thanks, > Dave > > > ------------------------------------------------------------------------------ > 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 > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ 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
