I agree with the new MMFF95s default, most of our common cases are modeled well with planar aromatic nitrogens.
About the dielectric, I don't have strong opinions. Depending on the scenario, I would consider either vacuo (1) or water (80) to be good choices, but 4 is a 'close enough approximation' of 1. S On 9/22/19 5:11 PM, Geoffrey Hutchison wrote: > While it's possible to change the force field with the -gen3d option, most > people don't. > > I think for 3.0 it might be nice to: > - Use MMFF94s (i.e., the one with planar aromatic nitrogens) > - Use a default dielectric constant of ~4.0 > > In my testing #1 helps a bit - and #2 at least doesn't hurt when comparing to > experimental crystal structures. > > Thoughts? > > -Geoff > > _______________________________________________ > OpenBabel-Devel mailing list > openbabel-de...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- Stefano Forli, PhD Assistant Professor Center for Computational Structural Biology Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
