Many atom types, such as heavy metal ions, were not included in the force field calibration because experimental data was not available for complexes that include these atoms. If you need to use these atom types in your application, you will need to estimate 4 atomic parameters for each atom type to be added. You will need to create a modified atomic parameter file containing the new types. Finally, you will need to direct AutoGrid and AutoDock to use the modified atomic parameter file instead of the default values included internally in the programs.
The default atomic parameter file, AD4.1_bound.dat, is available online here.
For metal ions, an example entry in the parameter file is:
atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4
The first four numbers are the ones to change:
Rii = sum of vdW radii of two like atoms (in Angstrom)
epsii = vdW well depth (in Kcal/mol)
vol = atomic solvation volume (in Angstrom^3) (4/3*pi*(Rii/2)**3)
solpar = atomic solvation parameter
Then, in the parameter files for AutoGrid and AutoDock (*.gpf and *.dpf files), add this command at the top of the file:
parameter_file <modified parameter file name>
A full description of these files is included in the AutoDock4.2 User Guide.
A good practice would be to validate these parameters by testing if docking results can reproduce any kind of experimental data, such as crystallographic coordinates and/or binding affinity trends in a series of molecules with known activity.