> * Are there cases where MMFF94s should be preferred to Ghemical?

Everything. The heuristic should be something like "MMFF94 if it works, UFF 
otherwise." Ghemical is included for backwards-compatibility -- it was much 
easier to implement than MMFF94.

> * Is GAFF particularly good at any systems that the others handle poorly?

It's the "Generalized Amber Force Field." It should be fairly good with 
proteins, but I don't think it's been tuned for speed as much as MMFF94 and UFF 
have been.

-Geoff
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