Have been looking at doing some dockings with a protein containing some calcium atoms. A couple years ago I had problems doing this in Autodock, however after speaking so the guys on the autodocking bulletin board I have found the following:

As far as I can gather the current situation is that ADT now recognises the calcium atom so long as it is labeled in the normal way in the pdb file and automatically assigns Rij and Rii from the AD4_parameters.dat file, HOWEVER does not assign a charge to the atom which you have to do manually by editing the pdbqt file.

This then raises the question what the charge on the calcium atom should be? A couple years ago Garrett suggested using the formal charge of 2+, however I am not certain this is strictly correct. In my case the calcium atom is coordinated by six protein ligands and the small molecule I am trying to dock in the classic calcium pentagonal bipyrimidal geometry. Given the proximity of six oxygens surely the apparent charge on the calcium that the small molecule is seeing will be substantially less than +2? Furthermore surely the presence of such a highly charged atom will affect the charge on these residues and thus alter the electrostatics of the binding site? Wouldn't it be far more accurate for the charge calculation to take into account the presence of the calcium atom (and presumably also the pH)? It feels like a bit of a fudge to manually edit the pdbqt file to the approximate value.

Incidentally I have compared dockings with the calcium charge set to +2 and 2/7. At +2 the electrostatics completely dominate the binding whilst at 2/7 the ligand is never in the correct orientation (as compared to my 1.8A X-ray structure).