you can not dock metal compound directly, because it is not added in the library of Autodock. To do so you have to add that compound in the Autodock library.

Here is the link which may help you to adding data in libraray:

http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Scientific%20Questions

Here is a published paper which can help you

http://autodock.scripps.edu/news/successfully-docking-to-proteins-with-metal-ions/

How can I dock metal compounds in AutoDock?. Available from: https://www.researchgate.net/post/How_can_I_dock_metal_compounds_in_AutoDock [accessed Mar 30, 2015].

Dear Mohana

I hope this message finds you in good health and spirit.

For molecular docking of a metal into an interested receptor, you can use of Molegro virtual DOCKER software. It’s really easy and favorable. Also for this issue you can use of MOE package easily. In agreement with Mr. Saxena, you can also consider AutoDock program for this issue. Also, the following tools can help you:

1-      LigandFit/Cerius2 4.10

2-      FlexX (in SYBYL 7.0)

Among these tools, AutoDock and Molegro are the most reliable in molecular docking.

All the best!

Have great day!

Res. Ass. Hassan Rasouli

Medical Biology Research Center, Kermanshah University of Medical Science

Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques

October 2017Journal of Computational Chemistry

DOI: 10.1002/jcc.25080