FlexPepDock in RosettaScripts keeps running

[Anonymous]

I’m using FlexPepDock in RosettaScripts:

Sometimes the job keeps on running and doesn’t stop. As you will see in the output below, FlexPepDock has it’s own internal filters and it seems it just keeps on trying to pack until it passes these filters. I’m running a mutate-then-dock protocol and for mutants where the receptor has several bulky residues the filters are never passed. If some poses aren’t going to output structures I just want the job to stop instead of it running forever (forever = 9 hours instead of 1 minute).

I’ve never had this problem with the stand along executable of FlexPepDock, so investigated a bit and outputed the structures from RosettaScripts that were not working (at the step right before they were docked) and docked them using the executable. They worked – all 180 of them. Before docking these structures had very positive total scores (from fa_rep and fa_atr), after docking it had decreased. The command line settings I used were the same: -pep_refine -peptide_chain B -receptor_chain A

I have my own filters in RosettaScipts and could apply them before docking to check if there are clashes or a positive total score, but I don’t want to filter these out necessarily as after docking some of them this had resolved many clashes. Is there any way to bypass these FlexPepDock filters, or kill the job if they don’t pass after many attempts.In the source code there is a part that mentions a score_filter (around line 659).

#############FAILED FILTER##############
core.pack.pack_rotamers: (0) built 17 rotamers at 4 positions.
core.pack.pack_rotamers: (0) IG: 4536 bytes
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: (0) built 16 rotamers at 4 positions.
core.pack.pack_rotamers: (0) IG: 4484 bytes
protocols.moves.RigidBodyMover: (0) Translate: Jump (before): RT -0.00995485 -0.997142 0.0748938 0.436191 0.0630658 0.897642 -0.899799 0.0416039 0.434316 1.62709 3.72141 -0.997627
protocols.moves.RigidBodyMover: (0) Translate: Jump (after): RT -0.00995485 -0.997142 0.0748938 0.436191 0.0630658 0.897642 -0.899799 0.0416039 0.434316 908.195 -370.066 195.007
FlexPepDockingPoseMetrics: (0) Isc: -2.95029
FlexPepDockingPoseMetrics: (0) Total BSA is: 472.409
FlexPepDockingPoseMetrics: (0) Interface HB #: 4
FlexPepDockingPoseMetrics: (0) Total packstats: 0.0892023
FlexPepDockingPoseMetrics: (0) Interface Unsat polar groups: 4
FlexPepDockingPoseMetrics: (0) 81 bsa: 204.522 HB: 2 pack: 0.434508 unsat: 1
FlexPepDockingPoseMetrics: (0) 82 bsa: 79.8592 HB: 2 pack: 0.57995 unsat: 0
FlexPepDockingProtocol: (0) Applying score filter 1
FlexPepDockingProtocol: (0) Failed filters – trying again
core.pack.task: (0) Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: (0) built 20 rotamers at 4 positions.
core.pack.pack_rotamers: (0) IG: 4668 bytes
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()

############PASSED FILTER#####################
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.task: (0) Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: (0) Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: (0) built 14 rotamers at 4 positions.
core.pack.pack_rotamers: (0) IG: 3952 bytes
protocols.moves.RigidBodyMover: (0) Translate: Jump (before): RT 0.230766 -0.929447 0.28788 -0.0663572 0.280144 0.957662 -0.970744 -0.240099 0.00297225 0.133068 4.79236 -1.12178
protocols.moves.RigidBodyMover: (0) Translate: Jump (after): RT 0.230766 -0.929447 0.28788 -0.0663572 0.280144 0.957662 -0.970744 -0.240099 0.00297225 890.292 -389.505 227.236
FlexPepDockingPoseMetrics: (0) Isc: -5.19865
FlexPepDockingPoseMetrics: (0) Total BSA is: 523.239
FlexPepDockingPoseMetrics: (0) Interface HB #: 6
FlexPepDockingPoseMetrics: (0) Total packstats: 0.0194762
FlexPepDockingPoseMetrics: (0) Interface Unsat polar groups: 5
FlexPepDockingPoseMetrics: (0) 81 bsa: 235.92 HB: 4 pack: 0.942534 unsat: 3
FlexPepDockingPoseMetrics: (0) 82 bsa: 91.4932 HB: 2 pack: 0.415633 unsat: 18446744073709551615
FlexPepDockingProtocol: (0) Applying score filter 1
protocols.moves.RigidBodyMover: (0) Translate: Jump (before): RT 0.230766 -0.929447 0.28788 -0.0663572 0.280144 0.957662 -0.970744 -0.240099 0.00297225 0.133068 4.79236 -1.12178
protocols.moves.RigidBodyMover: (0) Translate: Jump (after): RT 0.230766 -0.929447 0.28788 -0.0663572 0.280144 0.957662 -0.970744 -0.240099 0.00297225 890.292 -389.505 227.236
FlexPepDockingPoseMetrics: (0) Isc: -5.19865
FlexPepDockingPoseMetrics: (0) Total BSA is: 523.239
FlexPepDockingPoseMetrics: (0) Interface HB #: 6
FlexPepDockingPoseMetrics: (0) Total packstats: 0.035991
FlexPepDockingPoseMetrics: (0) Interface Unsat polar groups: 5
FlexPepDockingPoseMetrics: (0) 81 bsa: 235.92 HB: 4 pack: 0.942534 unsat: 3
FlexPepDockingPoseMetrics: (0) 82 bsa: 91.4932 HB: 2 pack: 0.415633 unsat: 18446744073709551615
protocols.rosetta_scripts.ParsedProtocol: (0)
}
=======================END MOVER FlexPepDockingProtocol=======================
protocols.rosetta_scripts.ParsedProtocol: (0) =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol: (0)
}

[Anonymous]

Try passing a large value to flexPepDocking::score_filter. Your log file says “FlexPepDockingProtocol: (0) Applying score filter 1”; 1 is a decimal value (filter value of 1.0 score units), not a count. So if you make it 100, or a 1000000, it will filter on higher values instead.

The code has a strange bypass that a filter of precisely 10000 will disable score filtering entirely (likely the same as just setting a filter to a huge number anyway…)

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