Yoshinobu Ishikawa
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.
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