[Dock-fans] Possible problem with DOCK 3.7 post processing scripts

Corey Taylor corey.taylor at uni-marburg.de
Thu Sep 27 02:30:31 PDT 2018


Cheers Trent, that did the trick. Will update our own Wiki accordingly.

Corey.

On 09/26/2018 07:00 PM, Trent E. Balius wrote:
>
> Thanks Corey for alerting us to your observation.  I think that we 
> need to describe this better in the tutorials.
>
> The rule of thumb is to make sure the energy cutoff when running 
> extract all is less than the energy cutoff for writing to the mol2 
> file during docking (the mol2_score_maximum parameter).
>
> for example, if mol2_score_maximum = -10  (this is the default value)
>
> then run:
>
> $DOCKBASE/analysis/extract_all.py -s -10
>
> or:
>
> $DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extact_all.txt -10
>
> This should circumvent the problem of having to rerun DOCK.
>
> I hope this helps,
>
> Trent
>
> ======================================
> Trent E. Balius, PhD
> Associate Specialist, Shoichet Lab,
> Dept. Pharm. Chem., UCSF
> Phone: (415) 514-4253
> URL: http://docking.org/~tbalius
> ======================================
>
> Error message from the attracted file:
>
> reading list of identifiers from file: extract_all.sort.uniq.txt
> reading extract info from ./extract_all.txt
> getting up to  1  poses for each of  341  ligands
> gathering poses for molecule FRAGID_0151
> reading extract info from ./extract_all.sort.uniq.txt
> <SNIP>
> gathering poses for molecule FRAGID_0364
> gathering poses for molecule FRAGID_0356
> gathering poses for molecule FRAGID_0184
> Traceback (most recent call last):
>   File "/nfs/kolblab_progs/bin/DOCK-3.7.2rc1/analysis/getposes.py", 
> line 358, in <module>
>     main(sys.argv)
>   File "/nfs/kolblab_progs/bin/DOCK-3.7.2rc1/analysis/getposes.py", 
> line 355, in main
>     bbndist=options.bbndist, bbndof=options.bbndof)
>   File "/nfs/kolblab_progs/bin/DOCK-3.7.2rc1/analysis/getposes.py", 
> line 192, in getPoses
>     receptors, realRank, part, scoreToCheck, newRecScore, cache)
>   File "/nfs/kolblab_progs/bin/DOCK-3.7.2rc1/analysis/getposes.py", 
> line 111, in getOnePose
>     cachedPoses = getPosesCache(file, molnum, id, rank, cache)
>   File "/nfs/kolblab_progs/bin/DOCK-3.7.2rc1/analysis/getposes.py", 
> line 92, in getPosesCache
>     returnItem = marshal.loads(cacheDict[str([molnum, id, rank])])
>   File 
> "/nfs/kolblab_progs/Anaconda_x64/lib/python2.7/bsddb/__init__.py", 
> line 270, in __getitem__
>     return _DeadlockWrap(lambda: self.db[key])  # self.db[key]
>   File 
> "/nfs/kolblab_progs/Anaconda_x64/lib/python2.7/bsddb/dbutils.py", line 
> 68, in DeadlockWrap
>     return function(*_args, **_kwargs)
>   File 
> "/nfs/kolblab_progs/Anaconda_x64/lib/python2.7/bsddb/__init__.py", 
> line 270, in <lambda>
>     return _DeadlockWrap(lambda: self.db[key])  # self.db[key]
> KeyError: "[334, 'FRAGID_0184', 1]"
>
>
>
>
>
>
> -----Original Message-----
> From: Corey Taylor <corey.taylor at uni-marburg.de>
> To: dock-fans <dock-fans at docking.org>
> Sent: Wed, Sep 26, 2018 9:06 am
> Subject: [Dock-fans] Possible problem with DOCK 3.7 post processing 
> scripts
>
> Dear all,
>
> We are using DOCK-3.7.2rc1 (cheers, John) and I believe I've bumped into
> a problem with the post-processing scripts. Excuse my ignorance of the
> actual mechanisms of the scripts, I'm mainly guessing.
>
> The getposes.py script exited with the attached error. Eventually I
> figured out that the pose it crashed on whilst trying to extract (in
> this case, a molecule named "FRAGID_0184") was in the extraction
> databases (extract_all.sort.uniq.txt, etc.) but not in test.mol2.gz so,
> of course, the retrieval failed. This error was repeated whether I used
> extract_all.py or extract_all_blazing_fast.py prior to running 
> getposes_py.
>
> Of course, the problem is fixed by simply making sure the default INDOCK
> parameter 'mol2_score_maximum' (-10.0) is set high (+10.0) as per the
> bkslab Wiki
> (http://wiki.bkslab.org/index.php/DOCK_3.7_2018/06/05_abl1_Tutorial) and
> running the dock again to ensure poses written to test.mol2.gz match
> what end up in the extraction files later.
>
> I may have missed a script parameter here so please advise if so or any
> other way I haven't thought of to head-off having to re-run the entire
> dock again or something similar. Mine was a very small dock so little
> harm done but I dread the idea of someone else having to re-run a big
> multi-day dock, hence I'm advising you guys of this in case there's a
> more elegant solution possible for the scripts themselves.
>
> Cheers guys,
>
> -- 
> Corey Taylor
> Kolb Lab
> Institute of Pharmaceutical Chemistry
> Philipps-University Marburg
> Marbacher Weg 6
> 35032 Marburg
> Germany
>
> Mailto: corey.taylor at uni-marburg.de
> Ph: +49 6421 28 21351
> Web: http://www.kolblab.org/taylor.html
>
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-- 
Corey Taylor
Kolb Lab
Institute of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6
35032 Marburg
Germany

Mailto: corey.taylor at uni-marburg.de
Ph: +49 6421 28 21351
Web: http://www.kolblab.org/taylor.html

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