Reply To: -dock_pert problem

[Anonymous]

Thanks for the suggestions. You are correct, I am docking the protein containing chains EF to protein with chains ABCD. The chain that moves 500angstroms compared to the input structure is chain EF.

To try to avoid clashes I have tried moving the two proteins apart by several increments, from a few angstroms to ~20 angstroms (at closest contact) away from each other and tried decreasing the -dock_pert perturbation sizes and tried doing prepacking. I have also varied the number of inner and outer cycles in the adaptive moves using the -docking:docking_centroid_inner/outer_cycles flags.

Occaisionally, if I start the proteins ~7 angstroms from each other and increase the number of outer and inner cycles by 5x the default values to 50 outer and 250 inner cycles respectively, I get 1 or 2 structures out of every 15-20 that will be closer than the typical 500 angstroms. These structures actually form an interface with the protein but still have a centroid RMS of ~100-150angsroms which is significantly greater than the 0-8 angstrom perturbations I’m shooting for.

Looking at the output the problem does seem to be in the Low-resolution rigid body moves. I’m not sure why it thinks it is failing in moving away… Below is partial output from a run w/ -dock_pert 3 4, outercycles = 100, innercycles = 50:

…

protocols.docking.DockingProtocol: Setting docking foldtree

protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 229 -1 EDGE 1 230 1 EDGE 230 458 -1 EDGE 1 459 2 EDGE 459 687 -1 EDGE 1 688 3 EDGE 688 916 -1 EDGE 1 917 4 EDGE 917 1255 -1 EDGE 1 1256 5 EDGE 1256 1319 -1

protocols.docking.DockingProtocol:

protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 229 -1 EDGE 229 230 1 EDGE 230 458 -1 EDGE 458 459 2 EDGE 459 548 -1 EDGE 548 687 -1 EDGE 548 1148 4 EDGE 687 688 3 EDGE 688 916 -1 EDGE 1148 917 -1 EDGE 1148 1255 -1 EDGE 1255 1256 5 EDGE 1256 1319 -1

protocols.docking.DockingProtocol:

protocols.docking.DockingInitialPerturbation: Reading options…

protocols.docking.DockingInitialPerturbation: dock_pert: true

protocols.docking.DockingInitialPerturbation: option[ docking::dock_pert ]()4 3

core.io.database: Database file opened: /usr/global/rosetta/rosetta3.1/rosetta_database/env_log.txt

core.io.database: Database file opened: /usr/global/rosetta/rosetta3.1/rosetta_database/cbeta_den.txt

core.io.database: Database file opened: /usr/global/rosetta/rosetta3.1/rosetta_database/pair_log.txt

core.io.database: Database file opened: /usr/global/rosetta/rosetta3.1/rosetta_database/cenpack_log.txt

protocols.docking.DockingInitialPerturbation: sliding into contact

protocols.docking.DockingInitialPerturbation: Moving away

protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.689405 0.597832 -0.409046 0.661045 0.750135 -0.0177809 0.296209 -0.282656 -0.912341 -23.3265 -22.274 48.2585

protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.689405 0.597832 -0.409046 0.661045 0.750135 -0.0177809 0.296209 -0.282656 -0.912341 -23.8252 -22.5823 49.0686

protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.689405 0.597832 -0.409046 0.661045 0.750135 -0.0177809 0.296209 -0.282656 -0.912341 -23.8252 -22.5823 49.0686

protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.689405 0.597832 -0.409046 0.661045 0.750135 -0.0177809 0.296209 -0.282656 -0.912341 -24.3239 -22.8905 49.8787

…

continues for a total 1000 lines of RigidBodyMover

…

protocols.docking.DockingInitialPerturbation: failed moving away with original vector. (:exclaim:)

Aborting DockingSlideIntoContact. (:exclaim:)(:eek:)(:exclaim:)

protocols.docking.DockingProtocol: finished initial perturbation

protocols.TrialMover: Acceptance rate: 1

protocols.TrialMover: Acceptance rate: 1

protocols.TrialMover: Acceptance rate: 1

protocols.TrialMover: Acceptance rate: 1

…

continues for a total 100 lines of TrialMover. (acceptance rate always = 1)

…

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

protocols.docking.DockingHighRes: in DockingHighRes.apply
protocols.docking.DockingHighRes: DOCK_MCM

core.pack.task: Packer task: initialize from command line()

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.pack_rotamers: built 0 rotamers at 0 positions.

core.pack.pack_rotamers: IG: 480 bytes

protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!!

protocols.geometry.RB_geometry: calling centroids_by_jump…

core.pack.task: Packer task: initialize from command line()

protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!!

…

…Repeats…

…

protocols.geometry.RB_geometry: centroids_by_jump_int called but no interface detected!!
protocols.geometry.RB_geometry: calling centroids_by_jump…
core.pack.task: Packer task: initialize from command line()
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.826737 0.503775 0.250432 0.527971 0.848495 0.0361073 -0.194301 0.162072 -0.967461 -272.794 -177.095 452.414
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.826737 0.503775 0.250432 0.527971 0.848495 0.0361073 -0.194301 0.162072 -0.967461 -770.71 -485.262 1263.04
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.826737 0.503775 0.250432 0.527971 0.848495 0.0361073 -0.194301 0.162072 -0.967461 -272.794 -177.095 452.414
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.826737 0.503775 0.250432 0.527971 0.848495 0.0361073 -0.194301 0.162072 -0.967461 -770.71 -485.262 1263.04
protocols.jobdist.main: Finished NC0_0001 in 505 seconds.

It looks like it doesn’t think it is succeeding in moving away and thus it aborts sliding the ligand protein (chains EF) back towards the Receptor. Any thoughts as to what is causing this and/or how to prevent it?