Hello! I'm trying to run add some missing loop to my protein by appear segmentation fault as error.
Anyone have an idea to solve this issue?
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core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712
core.init: command: /usr/local/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/remodel.static.linuxgccrelease -database /usr/local/rosetta_bin_linux_2021.16.61629_bundle/main/database/ -s ./5y0m.pdb -run:chain A -remodel:use_blueprint_sequence -remodel:blueprint ./5y0m_missmidd1_loop.remodel -ex1 -ex2 -use_input_sc -overwrite
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1681972652 seed_offset=0 real_seed=1681972652
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1681972652 RG_type=mt19937
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.61 seconds.
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ./5y0m.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ./5y0m.pdb
core.import_pose.import_pose: File './5y0m.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'GOL' from the PDB components dictionary for residue type 'pdb_GOL'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'PO4' from the PDB components dictionary for residue type 'pdb_PO4'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'CL' from the PDB components dictionary for residue type 'pdb_CL'
protocols.forge.remodel.RemodelMover: apply(): entered RemodelMover apply(). pose.size(): 679
protocols.forge.remodel.RemodelMover: 679
protocols.forge.remodel.RemodelMover: apply(): input PDB dssp assignment: (based on start structure)
protocols.forge.remodel.RemodelMover: LLLLLELLLLLLLLLHHHLLLLLEELLLLEEEELLLLLLEEEEEEELLLLEEEEEEEEEEEEEEEEEEEELLLLEELLLLEEEEEEEELLHHHHHHHHHHHHHHHHHHLLLLLLHHHLLLEEEEELLLLLLLLLLLLLLHHHHHHHHHLLELLEEEEELLHHHLLLEELLLLHHHLEELLEEEEEEEELLEEEEEEEEEELLLEEELLLLLEEELLEELLLLEELLHHHHHHHHHHHHLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHLLEELLLLLLLEEEEEEEEEEEELLLLLLLELLELLLLLHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLELLLLLLLLHHHLLLLLEELLLLEEEELLLLLLEEEEEEELLLLEEEEEEEEEEEEEEEEEEELLLLLEELLLLEEEEEEEELLHHHHHHHHHHHHHHHHHHLLLLLLHHHLLLEEEEELLLHHHLLLLLLLLHHHHHHHHHLLEELEEEEELLHHHLLLEELLLLHHHLEELLEEEEEEEELLEEEEEEEEEELLLEEELLLLLEEELLEELLLLEELLHHHHHHHHHHHHLLLEEEEEEEEEELLLHHHHHHHHHHHHHHHHLLEELLLLLLLLEEEEEEEEEEELLLLLLLELLELLLLLHHHHHHHHHHHHHHHHHHHHLLLLLLLLLL
protocols.forge.remodel.RemodelMover: apply(): reading blueprint file
protocols.forge.remodel.RemodelData: Found token 11 on blueprint line '11'
protocols.forge.remodel.RemodelData: Found token V on blueprint line '11'
protocols.forge.remodel.RemodelData: Found token L on blueprint line '11'
protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '11'
protocols.forge.remodel.RemodelData: Found token V on blueprint line '11'
protocols.forge.remodel.RemodelData: Do remodeling on chain A
protocols.forge.remodel.RemodelData: design position 11 to V VAL
protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '12'
protocols.forge.remodel.RemodelData: Found token x on blueprint line '12'
protocols.forge.remodel.RemodelData: Found token L on blueprint line '12'
protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '12'
protocols.forge.remodel.RemodelData: Found token F on blueprint line '12'
protocols.forge.remodel.RemodelData: Do remodeling on chain A
protocols.forge.remodel.RemodelData: design position 12 to F PHE
protocols.forge.remodel.RemodelData: Found token 12 on blueprint line '13'
protocols.forge.remodel.RemodelData: Found token G on blueprint line '13'
protocols.forge.remodel.RemodelData: Found token L on blueprint line '13'
protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '13'
protocols.forge.remodel.RemodelData: Found token G on blueprint line '13'
protocols.forge.remodel.RemodelData: Do remodeling on chain A
protocols.forge.remodel.RemodelData: design position 13 to G GLY
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
Segmentation fault (core dumped)
(base) [mcileane@alanine Nyl_dim]$ ls
5y0m.cif 5y0m_missing_loop.remodel 5y0m_missmidd1_loop.remodel 5y0m.pdb ROSETTA_CRASH.log
(base) [mcileane@alanine Nyl_dim]$ cat ROSETTA_CRASH.log