Segmentation Fault when using DockMCMProtocol

[Anonymous]

I was originally using the DockMCMProtocol in  PyRosetta.monolith.ubuntu.release-56 for ligand docking, however since downloading PyRosetta.monolith.ubuntu.release-84, a segmentation fault is returned when running the identical script that was used in release 56. I was wondering if anybody else has experienced the same issue or whether it is a known bug?

[Anonymous]

Can you post the script, or at least a simple version of it?  DocMCMProtocol is the main docking protocol and is tested in Rosetta, so it should be fine in PyRosetta.  It may be an input thing or something that changed with the foldtree.  

[Anonymous]

def dock_ligand(pose, partners='A_X', jobs=1, job_output ,cst_file):



# 1. Setup the docking FoldTree

dock_jump = 1

setup_foldtree(pose, partners, Vector1([dock_jump]) )



# 2. Create centroid <--> fullatom conversion Movers and a Mover to

#   recover sidechain conformations.

to_fullatom = SwitchResidueTypeSetMover('fa_standard')

recover_sidechains = ReturnSidechainMover(pose)



# 3. Make sure its full atom for high res docking

to_fullatom.apply(pose)



# 4. Create ScoreFunctions for centroid and fullatom docking and add

#    constraints.

scorefxn_ligand =  create_score_function('ligand')



set_constraints = ConstraintSetMover()

set_constraints.constraint_file(cst_file)



scorefxn_ligand.set_weight(atom_pair_constraint,1.5)

set_constraints.apply(pose)



# 5. Create a test pose

test_pose = Pose()



# 6. Setup the DockingProtocol

docking = DockMCMProtocol()

docking.set_scorefxn(scorefxn_ligand)



# 7. Setup the PyJobDistributor



jd = PyJobDistributor(job_output, jobs, scorefxn_ligand)

counter = 0



while (not jd.job_complete):

# A. Set necessary variables for this trajectory

test_pose.assign(pose)

counter+=1

test_pose.pdb_info().name(job_output+'_'+str(counter))



# B. Perform docking

docking.apply(test_pose)



# C. Output the decoy structure.

jd.output_decoy(test_pose)



return 

 

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