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
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
