Hi, Noel!
AFAIK, Ghemical FF ignores unsupported atoms at all (so you should fix the
atom's enviroment), UFF supports all elements, MMFF94 fails. Why you don't
want to use UFF for your problem? Of course, it is rather poor for
transition metals (but, of course, you may want to make some
constraints), but it is better than setting random values with risk to
obtain totally unreal initial geometry.
AFAIK, Avogadro uses openbabel to make FF optimizations, so you may need to
change something in openbabel to enforce Avogadro to use MMFF94 with
unsupported elements.
Yours,
Anton S. Lytvynenko.
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