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

[Prism Sciences]

John,
   You are correct that the surface in these regions is probably not a  
good site to dock.

I just did not expect that Dock would give that particular "error"  
when an attempted dock did not converge to a solution.  I would have  
expected that it just present the "best" fit regardless of how "bad"  
that solution was.  Dock does present a "solution" with a very large  
positive grid, es, or vdw score which does not correspond to an actual  
binding site, but just the "computational best fit" for that  
configuration.

I was expecting that for these poor docking areas to get solutions  
that were large and positive--bad fits.  But there were small areas  
that might be ok for binding, and it was better to just let dock try  
than just ignore those spots.

Any guidance on how to know that the solution just won't converge  
(i.e. no binding sites--and therefore interpret that error as  
representative of bad binding) vs. you need to increase the  
max_orientations because dock is "missing" a possible solution (i.e.  
the error means what it says it does).

Cheers,
--Jim

On Feb 24, 2009, at 4:09 PM, John J. Irwin wrote:

>
>
> 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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