HADDOCK cannot continue due to failed structures in it*

HADDOCK
1

some of our runs fail to finish correctly (this case in it1/water just before the end)
because docking of small nr of structures fails.

Do you have any general advice how to avoid that ?

best wishes, Eiso

this is the last part of haddock.out

[…]

Structure 110 124: running
Structure 116 129: failed
Structure 134 174: failed
Structure 153 82: failed
Structure 185 187: failed

Structure 116 129: failed
Structure 134 174: failed
Structure 153 82: failed
Structure 185 187: failed

The following structures have failed: [129, 174, 82, 187]
Only a flexible energy minimization will be performed.
Restarting structures…
Time-out of structure 129
Time-out of structure 174
Time-out of structure 82
Time-out of structure 187

HADDOCK cannot continue due to failed structures in it2
HADDOCK could not copy failed structures from previous iteration
The following structures could not be docked:
[129, 174, 82, 187]
##############################################################################
Finishing HADDOCK on: 2016-08-12 18:16:00
Au revoir.
Tot ziens.
Bye bye.
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…

2

Hi Eiso

It looks like even with only the minimization those structures are failing…
There must be a problem already in the it1 models.
Did you check the corresponding models in it1? Anything strange in them?

In principle you could download the full run, copy the missing it1 models into the water dir and restart a local version of haddock to complete the analysis.