Hey there,
I know that the forcefields only cover certain atoms (or is it atom
types?) and so setup will fail in some cases.
But shouldn’t the setup work if I set a problem atom as “fixed”, or
even “ignore”? This would be useful for preparing QM calculations
where I have some exotic metal centre, but some regular organic
ligands that I want to play with.
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.