Hello there is many tools to dock metal ions to protein. I can suggest you autodock, but you need to install it onto your computer.

May be MOE will be able to do it

. please check . not all docking tools can do this

Autodock might be suitable for your case.

dock.compbio.ucsf.edu/

Best

I think that all softwares above suggest very good. 

My related answer here may be helpful:

https://www.researchgate.net/post/Is_it_logical_to_use_Cu2_ion_as_receptor_and_a_protein_as_Ligand_assuming_the_protein_is_rigid

PyRx and Chimera should be easier.