[Dock-fans] Dock6 error -- Could not complete growth.

[John J. Irwin]

Prism Sciences wrote:
> Hello,
>    I do not understand the error I am getting from Dock.
>
> The error is listed in the .out files from executing dock6
>
> $ dock6 -i input.in -o output.out
>
> $ cat output.out
>
> <snip>
>   Elapsed time:  243 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
> </snip>
>
> I have been running a batch process that defines different 30x30x30  
> angstrom boxes around areas of interest on a protein.  Then attempts  
> to dock a specific ligand in that area.
> The results have been promising for several runs, but for a few  
> regions dock fails with the above error.
>   
Hi Jim

Did you look at the surface in the regions where this error occurs? 
There may be no good site to dock to.  It is not necessarily the case
that there will be a site everywhere you look.

John

> I have increased max_orientations from 1000 (works for the other  
> areas) to 2000, then 4000 with no luck.  But I know the grid box is  
> large enough to contain the ligand.
>
> The only difference in the input from a "good" run to the error runs  
> is the location of the box (a .pdb file), (which affects the .nrg  
> and .bmp files, obviously)
> The other issue is that the protein is largely tubular in form, the  
> "good" runs are along the waist, and the bad are at the ends.  Perhaps  
> the end is just too "rough" to converge to dock solution.
>
> I can continue to increase the max_orientations but I'm not sure why  
> this is happening, so I'm not sure I'm walking down the right path.
>
> Any suggestions?
>
> Cheers,
> --Jim Parker
>
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