[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.
Best,
Elaine
-----
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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