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

[John J. Irwin]

Hi Jim

Prism Sciences wrote:
> 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).
I don't have any guidance, except
a) it should be possible to automate what you seem to trying to do, by
having a script catch errors and fail gracefully when dock fails to
generate a solution.
b) sooner or later a reality check of just looking at the structure is
often helpful.
c) fully automatic docking protocols require careful tuning as the
variety of protein binding site pathologies (from a docking perspective)
seem endless.

Good luck and good docking

John
>
> 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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>