> 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. Several other people have suggested that Open Eye has a MMFF94 variant with no electrostatics, but repulsive VdW interactions. That seems a bit strange, but essentially means that they feel the vacuum electrostatics are too strong. In 3.0, the dielectric constant is adjustable via Python or C++ but I'd like a default, especially for the —gen3d operation, which is used heavily. In my tests, it doesn't have much effect, but YMMV. The -forcefield command-line "op" already has control over epsilon as well: https://github.com/openbabel/openbabel/blob/master/src/ops/forcefield.cpp -Geoff _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
