Docking ligands with exotic metals

[rjrich]

1. I have furnished the AMDock (linux) program with a modified dat file that contains parameters for Ruthenium (Ru) as follows:

atom_par Ru 4.04 0.010 34.5257 -0.00110 0.0 0.0 2 -1 -1 4 # Non H-bonding Ruthenium
atom_par RU 4.04 0.010 34.5257 -0.00110 0.0 0.0 2 -1 -1 4 # Non H-bonding Ruthenium

Furnishing the above parameters was sufficient to enable the docking to proceed. However, there was a warning message as follows:

"Unable to assign MAP type to atom Ru
Sorry, there are no Gasteiger parameters available for atom HB1_yas:B:HB11307:RU1
Unable to assign XYZ type to atom Ru
Unable to assign HYB type to atom Ru"

QUESTION: I am not sure how much it might matter to be able to provide Gasteiger parameters for Ruthenium, but would this be possible to do? What would I need to do to supply this additional information to the program? For example, if I were to use a quantum chemistry program such as Gaussian to determine partial atomic charges (e.g., Mulliken or Lowdin if not Gasteiger), could these be used? If so, how would I provide these charges to the docking program? Instead of partial atomic charges, would it be possible to use integer formal charges? For example, in my ligand, the oxidation state of Ru is Ru2+.

2. Which file formats can be used as input to AMDock for the receptor and the ligand? (e.g., pdb, sdf, mol2, xyz, etc.)

3. Can AMDock be used for virtual screening (e.g., of a multi-ligand sdf file) or inverse docking (one or a few ligands docked into an ensemble of receptors)?

4. Would it be possible for you to integrate Autodock-GPU into your AMDock program?

5. There might be a small bug in your software. The PDB files in the output could not be read by my main molecular viewer, YASARA-Structure. The ATOM/HETATM data has been placed in the wrong column starting with line 4. I was able to view the file after moving the column by one space.

Thank you for creating a program that is much easier to use than Autodock Tools!

-- RJR