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

[Prism Sciences]

John,
  Understand all.  Thanks for the help!

Cheers,
--Jim

On Feb 26, 2009, at 1:40 AM, John J. Irwin wrote:

> 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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>>>>
>>