> I would like to adjust the partial charges of zinc and the ligands
> in a protein enzymatic active site. I have the .pdb, I know
> precisely which ligands make up the coordination number (three HIS
> and one water). I have access to AmberTools and Gaussian 09. Is it
> possible to place the partial charges straight out of ab initio
> calculations into the Amber-99SB forcefield?
in general charges for chemically equivalent atoms are not
equivalenced in QM program outputs; so 'No' charges from QM outputs
are not used in force field library generation. Instead QM computed
electrostatic potential(s) is(are) exported into the program RESP,
that applies a series of restraints/constraints and among them charge
equivalencing for chemically equivalent atoms...
> From trawling through a lot of literature, manuals and old
> websites, I understand that I would need to use HF/6-31G* or
> B3LYP/6-31G* if I have a metal site. I suspect RESP and antechamber
> will be involved?
for a metal site I would use DFT based QM computation.
