> 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.
There are a variety of papers suggesting that the effective dielectric constant
inside a peptide is ~4.0. Most organic solvents are ~2-2.3 epsilon.
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 approximat
