[Chimera-users] Troubleshooting Docking Problem

[Elaine Meng]

Hi Alex,
If you look in the Help,  you can see that there is an option (default true) in receptor prep to omit chains that are made up of anything other than standard amino acids.  You could try changing that to “false”.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

Even if you try that, I do not know if Autodock Vina is meant for use with nucleic acids.  You may want to check their website for such information.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 13, 2019, at 2:50 PM, Alexandru Buhimschi <alexandru.buhimschi at yale.edu> wrote:
> 
> 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