AutoDock 4.0 has parameters for H, C, N, O, F, Mg, P, S, Cl, Ca, Mn, Fe, Zn, Br & I (that covers pretty much all of the routine docking atom types). If, however, you wish to introduce any other atom type (like Se), you'll need to add a new parameter file for this new atom type. 

It might be a bit tricky, but these links show you how this can be accomplished:

http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4

http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock

Hope that helps!

 Thanks you very much,

Mariya!!

Hi

If you have access to other docking soft like GLIDE or GOLD you can get more trustable result than autodock in the case of metal ligand.

Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques

October 2017Journal of Computational Chemistry

DOI: 10.1002/jcc.25080