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