I am attempting to learn ligand docking using autodock vina in Chimera. I am using a local copy of AutoDock Vina, and Chimera 1.9 (64 bit) for mac os 10.9.5. I have added H atoms to the ligand prior to loading the structure into Chimera. I added H atoms to the protein within Chimera. However, when I run AutpDock Vina I receive the error:

ValueError: Could not find atomic number for Ha Ha

failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors.

I thought that this could be because of the H atoms added to CA atoms are named HA by default, however if I change the HA atom names to H, I still get the same error. I can verify that there are no atoms named "Ha" in the structure. What am I doing wrong?

Thanks for your time.
--
William J. McDonald
Postdoctoral Scholar
Department of Chemistry and Biochemistry
University of California, Santa Cruz