Ensemble docking causes segmentation fault 11

[Anonymous]

Trying to locally dock two ensembles.

Docking runs fine with ensemble lists removed, but adding ensemble lists causes segmentation fault 11 on both mpi linux (Stampede) and MacOS. 

At output level 400 on Mac, it looks like the crash comes during the first cycle of low-res docking:

Suggestions?

 

protocols.docking.DockingLowRes: 

protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

protocols.docking.DockingLowRes: /// Ensemble 1: on                                                           ///

protocols.docking.DockingLowRes: /// Ensemble 2: on                                                           ///

protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::

protocols.moves.RigidBodyMover: Set movable jump# 1

core.conformation.Interface: Calculating protein-protein interface

core.conformation.Interface: Calculating protein-protein interface

core.scoring.DockingScoreFunction: unbound_energy -9.12546 full_score -22.3235 diff -13.198

core.conformation.Interface: Calculating protein-protein interface

core.conformation.Interface: Calculating protein-protein interface

core.scoring.DockingScoreFunction: unbound_energy -9.12546 full_score -22.3235 diff -13.198

core.conformation.Interface: Calculating protein-protein interface

core.conformation.Interface: Calculating protein-protein interface

core.conformation.Interface: Calculating protein-protein interface

core.scoring.DockingScoreFunction: unbound_energy -5.76637 full_score -19.9808 diff -14.2144

ens_local_dock.sh: line 17: 36464 Segmentation fault: 11  docking_protocol.macosclangrelease -in:path input -in:file:s RTA_F5_complex_aligned.pdb -in:file:native RTA_F5_complex_native.pdb -ensemble1 RTA.ensemble.list -ensemble2 F5.ensemble.list -partners A_B -dock_pert 3 8 -ex1 -ex2aro -out:path:all output -out:file:silent RTA_F5_ens_local_dock.o -overwrite -out:level 400 -score:docking_interface_score 1 -nstruct 1

[Anonymous]

Hello,

One source of this segfault could be not pre-packing your ensemble. Running the ‘docking_prepack_protocol’ executable not only pre-packs the members of the ensemble, but it also edits the ensemble lists with normalised energy scores that the ‘docking_protocol’ executable then uses to try out the various conformations in the ensemble.

A quick tutorial on how to use docking pre-pack (with option flags etc.) can be found here: https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking#docking-flexible-proteins.

Hope that helps.

If this doesn’t work, we might need to look at your ensemble inputs to check sequence length and chain order mismatches etc.

Shourya

[Anonymous]

Hello,

One source of this segfault could be not pre-packing your ensemble. Running the ‘docking_prepack_protocol’ executable not only pre-packs the members of the ensemble, but it also edits the ensemble lists with normalised energy scores that the ‘docking_protocol’ executable then uses to try out the various conformations in the ensemble.

A quick tutorial on how to use docking pre-pack (with option flags etc.) can be found here: https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking#docking-flexible-proteins.

Hope that helps.

If this doesn’t work, we might need to look at your ensemble inputs to check sequence length and chain order mismatches etc.

Shourya

[Anonymous]

Hello,

One source of this segfault could be not pre-packing your ensemble. Running the ‘docking_prepack_protocol’ executable not only pre-packs the members of the ensemble, but it also edits the ensemble lists with normalised energy scores that the ‘docking_protocol’ executable then uses to try out the various conformations in the ensemble.

A quick tutorial on how to use docking pre-pack (with option flags etc.) can be found here: https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking#docking-flexible-proteins.

Hope that helps.

If this doesn’t work, we might need to look at your ensemble inputs to check sequence length and chain order mismatches etc.

Shourya

[Anonymous]

Shourya:

Thanks. Prepack was the problem. This issue is resolved.

[Anonymous]

Shourya:

Thanks. Prepack was the problem. This issue is resolved.

[Anonymous]

Shourya:

Thanks. Prepack was the problem. This issue is resolved.

[Author]

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