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?