Hi Ganesh,

My problem is not molecular docking. As I mentioned I want to find a potential interaction between a ligand and a metal ion.

Thank you

Any standard ab initio modeling code should be able to do this. The problem is how well the theory you use can describe transition metals. This review should explain I think: http://pubs.rsc.org/en/Content/ArticleLanding/2009/CP/b907148b#!divAbstract  If your molecules are small enough doing coupled cluster in something like gaussian 09 or free alternatives like GAMESS (haven't use those) may work. 

Here some more comments:

https://lirias.kuleuven.be/bitstream/123456789/465002/1/dft_transition_metal_ann_rep_c.pdf

Hi,

The following paper may help you:

"Binding mode prediction and inhibitor design of anti-influenza virus diketo acids targeting metalloenzyme RNA polymerase by molecular docking"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124789/pdf/97320630006221.pdf

It's indeed a perfect task to be handled by an ab initio quantum mechanics tool. The level of theory would depend on the available computing resources.

You can use on-line molecular modelling software at www.chemosophia.com . Now free and fast

www.chemosophia.com