> > I am a little bit annoyed by the fact that the UFF energy > is not even negative and that the two FFs disagree by so much. >
I would not consider this to be a big problem, IMHO. Do the two FFs compute something different? > Yes, very much so. UFF, for example does not include electrostatic non-bonded terms, and MMFF94 does. Additionally, MMFF94 includes a specific term for hydrogen bonding interactions. I consider force field energies to only be relevant in relative terms. That is, taking the relative difference of energy of relative conformers using a force field is more useful than the absolute value. (And particularly comparing between numbers from UFF vs. MMFF94 vs. GAFF, etc.) Even then, while force fields are useful for “quick cleanup” as my group showed (https://doi.org/10.1002/qua.26381) the relative energy rankings of UFF and MMFF94 are still crude relative to ML or quantum methods. In other words, the question is “does optimizing a conformer with UFF or MMFF94 help?” Yes. In general, conformers generated using RDKit (or Open Babel .. or most methods I’ve seen) have lower RMSD when optimized by a force field. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/
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