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

Corey Taylor corey.taylor at uni-marburg.de
Wed Sep 26 09:06:08 PDT 2018

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

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

-------------- next part --------------
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
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>
  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]"

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