Reply To: Using Patches in Rosetta

[Anonymous]

First of all thanks for taking the time to bother with this problems!

Using the suggested patch in Abinitio centroid mode only resulted in following segmentation fault after Abinitio:

===================================================================
Finished Abinitio

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_SS_distance_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CaCbS_angle_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CbSSCb_dihedral_score
core.scoring.dunbrack: Dunbrack library took 0.06947 seconds to load from binary
Segmentation fault

Using a modified pdb file in the relax Application, the error message comes after following lines:

protocols.jd2.PDBJobInputter: filling pose from PDB FSH_S_a_000019073.pdb
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_SS_distance_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CaCbS_angle_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CbSSCb_dihedral_score
core.scoring.dunbrack: Dunbrack library took 0.068129 seconds to load from binary
core.pack.task: Packer task: initialize from command line()
core.pack.task: Packer task: initialize from command line()
protocols.relax.ClassicRelax:
protocols.relax.ClassicRelax:
protocols.relax.ClassicRelax:

===================================================================
protocols.relax.ClassicRelax: Stage 1
protocols.relax.ClassicRelax: Ramping repulsives with 8 outer cycles and 1 inner cycles
Segmentation fault

I assume it has something to do with the format of the pdb-file but I’m not quite sure.
Is there any other information that might be helpful!