[Chimera-users] Failed to prepare receptor for AutoDock Vina

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 9 16:43:21 PDT 2014

Hi William,
We usually can’t tell without your data, so if you are willing to share it, please use menu: Help… Report a Bug and attach the file or the receptor or perhaps a Chimera session with both the ligand and receptor to the report, with short description of the problem and your contact information.

It might be the data, or it might be a bug.  Suggesting the latter, when testing the Autodock Vina interface in Chimera 1.9 just today, I also had a preparation problem, but when I tried exactly the same structures in 1.8, I did not have the problem.

You could try getting Chimera 1.8 from our download page (you can give it a different name or put it in a different place than your other installation to avoid overwriting it) and seeing if that works.  Sorry for the difficulties.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 9, 2014, at 4:28 PM, William McDonald <pchem at ucsc.edu> wrote:

> Hello Chimera users,
> 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

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