On May 7, 2010, at 8:01 AM, Tim Vandermeersch wrote: >>> However, I can't see any reason not to treat 2D structures like 0D >>> ones. It works very well.
As long as the stereochemistry is preserved, I don't think it matters much. > No, sounds good. The reason why flat structures stay flat is an > optimization issue. If all forces are in a plane, there is no driving > force to make an atom move perpendicular to that plane. Perhaps we should add a step which slightly tweaks the dihedral angles before running MM? Cheers, -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
