Haddock_end_of_it1_failed

HADDOCK
1

Dear All,

My job crashed. I checked the haddock.out and there I found:

Structure 6: failed
Structure 12: failed
Structure 16: failed
Structure 20: failed
Structure 24: failed
Structure 34: failed
Structure 40: failed
Structure 44: failed
Structure 50: failed
Structure 54: failed
Structure 58: failed
Structure 64: failed
Structure 68: failed
Structure 72: failed
Structure 82: failed
Structure 88: failed
Structure 92: failed
Structure 98: failed
Structure 104: failed
Structure 108: failed
Structure 112: failed
Structure 116: failed
Structure 122: failed
Structure 126: failed
Structure 132: failed
Structure 140: failed
Structure 144: failed

The following structures have failed: [6, 12, 16, 20, 24, 34, 40, 44, 50, 54, 58, 64, 68, 72, 82, 88, 92, 98, 104, 108, 112, 116, 122, 126, 132, 140, 144]
Only a flexible energy minimization will be performed.
Restarting structures…
Time-out of structure 6
Time-out of structure 12
Time-out of structure 16
Time-out of structure 20
Time-out of structure 24
Time-out of structure 34
Time-out of structure 40
Time-out of structure 44
Time-out of structure 50
Time-out of structure 54
Time-out of structure 58
Time-out of structure 64
Time-out of structure 68
Time-out of structure 72
Time-out of structure 82
Time-out of structure 88
Time-out of structure 92
Time-out of structure 98
Time-out of structure 104
Time-out of structure 108
Time-out of structure 112
Time-out of structure 116
Time-out of structure 122
Time-out of structure 126
Time-out of structure 132
Time-out of structure 140
Time-out of structure 144

HADDOCK cannot continue due to failed structures in it1
HADDOCK could not copy failed structures from previous iteration
The following structures could not be docked:
[6, 12, 16, 20, 24, 34, 40, 44, 50, 54, 58, 64, 68, 72, 82, 88, 92, 98, 104, 108, 112, 116, 122, 126, 132, 140, 144]
##############################################################################
Finishing HADDOCK on: 2020-07-27 09:10:14
Au revoir.
Tot ziens.
Bye bye.
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…

Can you tell me what this message means and how to get rid of this error?

thanks
karol

2

You have many structures failing - probably indicating some issues in the starting structures, or a problem with your restraints.

If running locally you might clean the run (e.g. remove all it1 files in the run directory) and restart HADDOCK.

If running on the server, check carefully your input data.

3

Hi

thanks. I would say restraints as other run with different combination of the same restraints completed successfully. In this particular run that crashed, I dock with centroid restraints on both fixed and scanning probe. Both assigned to be unambiguous. This is not necessary true, as only, one of them, that is centroid of scanning probe, is really unambigous. And I think that it fails because centroid on fixed chain violates all other restraints to much. I will wait until other runs complete and based on that try to draw some conclusions. Please, do not close this ticket, as I might inquire with more specific comments in future.

kind regards
karol

4

HI

One question: I assume that when I use option of “Number of partitions for random exclusions” the code tries ALL possible combinations of these restraints? I mean: lets assume that I have 20 distance restraints and the “Number of partitions for random exclusion” = 5. This would mean that haddock runs 5 “parallel” runs, each time excluding 4 restraints or it runs ALL possible combinations of 5?

thanks

5

The restraints are randomly partitioned. In you example, for each model 5 restraints would be discarded.
But it is not a systematic evaluation of all combinations (would simply not be doable).

Also it is not 5 parallel runs, but one in which each model is using a different subset of the restraints.

6

Thank you very much. Very helpful.

cheers