Hello-

I have been trying to perform a docking search for small molecule binding to a B-DNA double helix (e.g. 1ZFH). Unfortunately, when I set up the ligand and receptor, I receive the following error:

IndexError: list index out of range

Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages.

cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors.

I am not sure what I can do to address this, but I have tried multiple DNA structures and the result appears to be the same.

I have also encountered this error which I could not resolve either:

ValueError: Could not find atomic number for Ha Ha
> failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors.

Please let me know if there is anything I should do to address this issue.

Best,
Alex