Hi,

As far as I know, there is no docking software you want.

Alternatively, you can try molecular dynamics simulation, which should tell you where Cd ions stay in the active site.

AMBER is a nice, popular program:

http://ambermd.org/

http://jswails.wikidot.com/installing-amber14-and-ambertools14

http://ambermd.org/tutorials/

You need to parameterize Cd ions for use in AMBER:

http://archive.ambermd.org/201108/0751.html

When thiol residues are in the active site, those should be de-protonated in your simulations.