I wouldn't recommend metal ion docking using auto dock due to its inability to correlate electronic structure theory. But yes you can obtain parameters from their official webpage.
New forcefield for AutoDock includes parameters for Zn (Article AutoDock4(Zn): An Improved Auto Dock Force Field for Small-M...
). For other ions, you need to add the parameters manually. Moreover, you need to optimize the partial charges on the metal ion. You may do that in a control experiment using a metal bound protein. In my experience, for a divalent cation, partial charge between +0.6 to +0.7 on the metal center produces almost correct coordination geometry.