[Chimera-users] Program close during AutoDock Vina Session

Conrad Huang conrad at cgl.ucsf.edu
Fri Jul 21 10:51:43 PDT 2017

Unfortunately, it is not possible to restore the Chimera session. 
However, you may be able to retrieve the output from Autodock Vina if 
you get help from NBCR.

The Autodock Vina service is actually provided by NBCR 
(http://nbcr.ucsd.edu/products/web-services) which uses the Opal Toolkit 
to handle remote requests.  When Chimera starts the Autodock Vina 
request, it prints out in the Reply Log the URL that NBCR returns for 
getting status and data files for the submitted job.  If you have that 
URL (Chimera keeps track of it for you and records it in saved session 
files), you can access your job via a browser, but it doesn't sound like 
you have access to that anymore.  The only way to recover that URL is 
for the NBCR web services administrator to look through the list of jobs 
(and I don't know how long they keep job data) and try to find your job 
using some identifying data, e.g., it will have input files named 
"receptor.pdbqt", "ligand.pdbqt" and "vina.conf"; perhaps you can also 
supply some information about the receptor and ligand molecules.  If 
they find the job (assuming that they are willing to do so and the job 
is still around), then they should be able to supply you with the access 
URL for the job.

If you do manage to get access to the job, the output file you want is 
named "results.pdbqt", which you should be able to open using the 
ViewDock tool.


On 7/21/2017 7:36 AM, Nannette Yount wrote:
> Hi,
> I had a computer shutdown during an Autodock Vina session (via Opal 
> server) during the “execution in progress” stage.  These sessions 
> typically take between 5-6 days to complete, and now upon computer 
> restart – when opening Chimera, I see no evidence that the session is 
> still ongoing.
> The “get information” icon – where I could check Autodock status is also 
> greyed out.
> Is there any way to get this session back – since it’s probably still 
> running on the server (process was about 3 days into the session)?
> Thanks,
> Nannette
> Nannette Y. Yount, Ph.D.
> Infectious Diseases
> Department of Medicine
> Harbor-UCLA
> Torrance, CA 90502
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