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Ensemble Docking with RosettaDock 4.0 Protocol

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Ensemble Docking with RosettaDock 4.0 Protocol


I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:

$ mpirun -np 24 --hostfile $PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags


I get the following output in ROSETTA_CRASH.log:


[FILE]: src/core/scoring/etable/count_pair/

[LINE]: 220


[ ERROR ] UtilityExitException

ERROR: Assertion `res2.is_bonded(res1)` failed.




However, the simulation still runs and I still get outputs... I don't know if my docked structures will suffer from this error, or if mt results are still reliable. Can someone help me to turn around this issue? 

Rosetta_crash.txt3.89 KB
dock_flags.txt466 bytes
Post Situation: 
Wed, 2022-07-27 07:00

In order to solve this problem, what I did was to:

  1. Relax input structures separetly with minimum outputs just to remove initial clashes.
  2. Using pymol, I created a complex (as specifiend in tutorials), and separate the complex and each chain separetly.
  3. With the pdbs of each chain separately I generated the ensembles.
Mon, 2022-09-26 07:50