Parameters

[Axel]

jack,

before putting too much effort into this, please note
that the compound you want to parametrize poses
several serious problems to quantum chemistry
calculations, particularly in but not restricted to DFT.

so any effort to parmetrization will be likely to yield
questionable results (this system has a complicated spin
structure which essentially needs a true multi-reference
calculation to get it right.). also, it is quite likely that
the parameters will not be overly helpful for equilibration.
it is probably best to just insert some fake non-bonded
parameters and make the whole enzymatic complex rigid.

if you have not done so, i would also strongly recommend
to practice with a simpler molecule (there are plenty tutorials
for all kinds of modeling packages).

cheers,
    axel.