[Dock-fans] Dock 6.6 error

Sudipto Mukherjee sudmukh at yahoo.com
Wed Dec 21 18:09:47 PST 2016


Hi Michael,
That error - "Could not complete growth" means that while individually growing and minimizing torsions, the DOCK algorithm reached a point where none of the partially grown conformers fit in the site any more. 
Could you run DOCK again with the verbose flag (-v)? This will provide details about the growth process during while growing each torsion.
If possible, please also attach all the files used so that we may reproduce the calculation and identify the problem.
Sudipto 

    On Thursday, December 22, 2016 4:31 AM, John Irwin <jir322 at gmail.com> wrote:
 

 forwarded to dock-fans at docking.org

On Wed, Dec 21, 2016 at 2:34 PM, Sacco, Michael
<michaelsacco at health.usf.edu> wrote:
> To whom this may concern,
>
>
> My name is Michael Sacco and I am a PhD student in the Chen lab at the
> University of South Florida College of Medicine. I'm currently encountering
> a problem with Dock 6.6 that I cannot resolve. I have spent a long time
> troubleshooting, yet I cannot figure out what is wrong. After submitting the
> dock6 command, I am receiving the following error message:
>
> "Elapsed time:  0 seconds
>
> ERROR:  Could not complete growth.
>          Confirm that the grid box is large enough to contain the ligand,
>          and try increasing max_orientations.
>
>
> 1 Molecules Processed
> Total elapsed time:    0 seconds"
>
> I have tried changing the maximum number of orientations, set orient ligand
> to "off", as well as followed the instructions that were offered online, all
> to no avail. Additionally, I tried docking a very small molecule and that
> did not fit either. My spheres are correctly placed, the box is of
> sufficient size, and the docking has been previously performed with Dock
> 3.5. I have attached my grid parameters, flexible docking input, receptor
> file, crystallized ligand, sphere file, and box file. I was wondering if you
> could take a look and let me know what you think? Any help would be greatly
> appreciated.
>
> Thanks a lot,
>
> Michael Sacco
>
>
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