[Chimera-users] Troubleshooting Docking Problem

[Alexandru Buhimschi]

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
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