Topobuilder segmentation fault

[Anonymous]

I’m following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I’m in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault. 

$ROSETTA3_HOME/bin/rosetta_scripts -parser:protocol make_fragments.xml -in:file:s sketch.pdb -parser:script_vars vall=/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz

I’m not changing sketch.pdb and not sure why I’m getting a segmentation fault.

core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags 

core.init: {0} Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184

core.init: {0} command: /usr/local/apps/rosetta/2021.16/bin/rosetta_scripts -parser:protocol make_fragments.xml -in:file:s sketch.pdb -parser:script_vars vall=/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz

basic.random.init_random_generator: {0} ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1942159844 seed_offset=0 real_seed=1942159844 thread_index=0

basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=1942159844 RG_type=mt19937

core.init: {0} found database environment variable ROSETTA3_DB: /usr/local/apps/rosetta/2021.16/main/database

protocols.jd2.PDBJobInputter: {0} Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: {0} PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: {0} pushed sketch.pdb nstruct index 1

protocols.evaluation.ChiWellRmsdEvaluatorCreator: {0} Evaluation Creator active … 

protocols.jd2.PDBJobInputter: {0} PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: {0} filling pose from PDB sketch.pdb

core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set.  Created 984 residue types

core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 1.18 seconds.

core.import_pose.import_pose: {0} File ‘sketch.pdb’ automatically determined to be of type PDB

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue VAL:NtermProteinFull 1

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG1 on residue VAL:NtermProteinFull 1

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG2 on residue VAL:NtermProteinFull 1

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ILE 2

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG1 on residue ILE 2

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG2 on residue ILE 2

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue ILE 2

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue SER 3

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OG  on residue SER 3

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ILE 4

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG1 on residue ILE 4

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG2 on residue ILE 4

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue ILE 4

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue VAL 5

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG1 on residue VAL 5

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG2 on residue VAL 5

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASN 6

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASN 6

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASN 6

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  ND2 on residue ASN 6

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE  on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH1 on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH2 on residue ARG 7

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue MET 8

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue MET 8

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  SD  on residue MET 8

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE  on residue MET 8

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OH  on residue TYR 9

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE  on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH1 on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH2 on residue ARG 10

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE1 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE3 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ2 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ3 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CH2 on residue TRP 11

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASN 12

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASN 12

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASN 12

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  ND2 on residue ASN 12

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ALA 13

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ILE 14

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG1 on residue ILE 14

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG2 on residue ILE 14

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue ILE 14

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue LYS 15

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue LYS 15

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue LYS 15

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE  on residue LYS 15

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NZ  on residue LYS 15

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLU 16

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLU 16

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLU 16

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLU 16

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE2 on residue GLU 16

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASN 17

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASN 17

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASN 17

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  ND2 on residue ASN 17

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASP 18

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASP 18

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASP 18

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD2 on residue ASP 18

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ALA 19

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue SER 20

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OG  on residue SER 20

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue MET 21

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue MET 21

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  SD  on residue MET 21

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE  on residue MET 21

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ALA 22

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASP 23

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASP 23

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASP 23

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD2 on residue ASP 23

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue PHE 24

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLN 25

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLN 25

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLN 25

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLN 25

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE2 on residue GLN 25

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASP 26

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASP 26

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASP 26

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD2 on residue ASP 26

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLU 27

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLU 27

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLU 27

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLU 27

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE2 on residue GLU 27

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue LEU 28

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue LEU 28

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue LEU 28

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue LEU 28

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASP 29

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASP 29

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASP 29

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD2 on residue ASP 29

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLU 30

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLU 30

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLU 30

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLU 30

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE2 on residue GLU 30

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue PHE 31

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue PHE 32

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue LYS 33

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue LYS 33

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue LYS 33

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE  on residue LYS 33

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NZ  on residue LYS 33

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE1 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE2 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE3 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ2 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ3 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CH2 on residue TRP 34

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ASP 35

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ASP 35

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD1 on residue ASP 35

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OD2 on residue ASP 35

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue LEU 36

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue LEU 36

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue LEU 36

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue LEU 36

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLN 37

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLN 37

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLN 37

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLN 37

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE2 on residue GLN 37

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE  on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CZ  on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH1 on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NH2 on residue ARG 38

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue ALA 39

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  ND1 on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE2 on residue HIS 40

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue LEU 41

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue LEU 41

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD1 on residue LEU 41

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue LEU 41

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue GLN 42

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue GLN 42

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD  on residue GLN 42

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OE1 on residue GLN 42

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE2 on residue GLN 42

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CG  on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  ND1 on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CD2 on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CE1 on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  NE2 on residue HIS 43

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 44

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  CB  on residue SER:CtermProteinFull 44

core.conformation.Conformation: {0} [ WARNING ] missing heavyatom:  OG  on residue SER:CtermProteinFull 44

core.pack.pack_missing_sidechains: {0} packing residue number 1 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 2 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 3 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 4 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 5 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 6 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 7 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 8 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 9 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 10 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 11 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 12 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 13 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 14 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 15 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 16 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 17 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 18 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 19 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 20 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 21 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 22 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 23 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 24 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 25 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 26 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 27 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 28 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 29 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 30 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 31 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 32 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 33 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 34 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 35 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 36 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 37 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 38 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 39 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 40 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 41 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 42 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 43 because of missing atom number 5 atom name  CB 

core.pack.pack_missing_sidechains: {0} packing residue number 44 because of missing atom number 6 atom name  CB 

core.pack.task: {0} Packer task: initialize from command line() 

core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015

core.scoring.etable: {0} Starting energy table calculation

core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well

core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)

core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)

core.scoring.etable: {0} Finished calculating energy tables.

basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv

basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv

basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv

basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv

basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv

basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt

basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.

basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat

core.scoring.elec.util: {0} Read 40 countpair representative atoms

core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true.

core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.

core.pack.dunbrack.RotamerLibrary: {0} Binary rotamer library selected: /usr/local/apps/rosetta/2021.16/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin

core.pack.dunbrack.RotamerLibrary: {0} Using Dunbrack library binary file ‘/usr/local/apps/rosetta/2021.16/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.

core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.29 seconds to load from binary

core.pack.pack_rotamers: {0} built 586 rotamers at 44 positions.

core.pack.pack_rotamers: {0} Requesting all available threads for interaction graph computation.

core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph

basic.thread_manager.RosettaThreadManager: {?} Creating a thread pool of 1 threads.

basic.thread_manager.RosettaThreadPool: {?} Launched 0 new threads.

core.pack.rotamer_set.RotamerSets: {0} Completed interaction graph pre-calculation in 1 available threads (1 had been requested).

protocols.rosetta_scripts.RosettaScriptsParser: {0} dock_design_filename=make_fragments.xml

protocols.rosetta_scripts.RosettaScriptsParser: {0} Variable substitution will occur with the following values: ‘%%vall%%’=’/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz’;  

protocols.rosetta_scripts.RosettaScriptsParser: {0} Substituted script:

<ROSETTASCRIPTS>

 <MOVERS>

  <PeptideStubMover name=”add_loops_ffd” reset=”false”>

   <Prepend anchor_atom=”N” anchor_rsd=”1″ connecting_atom=”C” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”12″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”13″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”14″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”26″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”27″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”28″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”29″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”30″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”31″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”43″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”44″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”45″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

<Insert anchor_atom=”C” anchor_rsd=”57″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

  </PeptideStubMover>

  <StructFragmentMover name=”makeFrags_ffd” prefix=”frags” vall_file=”/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz” output_frag_files=”1″

    large_frag_file=”frags.200.9mers” small_frag_file=”frags.200.3mers” frag_weight_file=”scores.cfg”/>

 </MOVERS>

 <PROTOCOLS>

  <Add mover=”add_loops_ffd”/>

  <Add mover=”makeFrags_ffd”/>

 </PROTOCOLS>

</ROSETTASCRIPTS>

protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts…

protocols.rosetta_scripts.RosettaScriptsParser: {0} …done

protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator…

protocols.rosetta_scripts.RosettaScriptsParser: {0} …done

protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script…

protocols.rosetta_scripts.RosettaScriptsParser: {0} …done

protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:

<ROSETTASCRIPTS>

    <MOVERS>

        <PeptideStubMover name=”add_loops_ffd” reset=”false”>

            <Prepend anchor_atom=”N” anchor_rsd=”1″ connecting_atom=”C” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”12″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”13″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”14″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”26″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”27″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”28″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”29″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”30″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”31″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”43″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”44″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”45″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

            <Insert anchor_atom=”C” anchor_rsd=”57″ connecting_atom=”N” jump=”false” repeat=”1″ resname=”GLY”/>

        </PeptideStubMover>

        <StructFragmentMover frag_weight_file=”scores.cfg” large_frag_file=”frags.200.9mers” name=”makeFrags_ffd” output_frag_files=”1″ prefix=”frags” small_frag_file=”frags.200.3mers” vall_file=”/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz”/>

    </MOVERS>

    <PROTOCOLS>

        <Add mover=”add_loops_ffd”/>

        <Add mover=”makeFrags_ffd”/>

    </PROTOCOLS>

</ROSETTASCRIPTS>

core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015

core.scoring.etable: {0} Starting energy table calculation

core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well

core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)

core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)

core.scoring.etable: {0} Finished calculating energy tables.

basic.io.database: {0} Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine

basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt

basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt

basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt

basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt

basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt

basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt

core.scoring.ramachandran: {0} shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat.

basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat

core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat.

protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named “add_loops_ffd” of type PeptideStubMover

protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named “makeFrags_ffd” of type StructFragmentMover

protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following settings

protocols.rosetta_scripts.ParsedProtocol: {0} Added mover “add_loops_ffd”

protocols.rosetta_scripts.ParsedProtocol: {0} Added mover “makeFrags_ffd”

protocols.jd2.PDBJobInputter: {0} PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: {0} filling pose from saved copy sketch.pdb

protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER PeptideStubMover – add_loops_ffd=======================

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

Segmentation fault

Rosetta crash.log

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2021.16+release.8ee4f02

[COMMIT_DATE]: 2021-04-20T20:57:38.289184

[APPLICATION]: /usr/local/apps/rosetta/2021.16/bin/rosetta_scripts

[MODE]: Release

[EXTRAS]: cxx11thread 

[OS]: GNU/Linux

[COMPILER]: GCC version “9.2.0”

[STDLIB]: libstdc++ version 20190812

[START_OPTIONS]

 -in:file:s=sketch.pdb -parser:protocol=make_fragments.xml -parser:script_vars=vall=/usr/local/apps/rosetta/2021.16/main/tools/fragment_tools/vall.jul19.2011.gz

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x24) [0x2aaab8e15354]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libutility.so(utility::signal_handler(int)+0xd4) [0x2aaab8e15464]

/lib64/libc.so.6(+0x362f0) [0x2aaaba9962f0]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols_a.6.so(protocols::cyclic_peptide::PeptideStubMover::handle_termini_and_store_terminal_dihedrals(core::pose::Pose&, unsigned long, unsigned long, unsigned long, unsigned long&, double&, double&, double&, double&, bool&, bool&)+0x182) [0x2aaaae107652]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols_a.6.so(protocols::cyclic_peptide::PeptideStubMover::append_by_bond(core::pose::Pose&, unsigned long, core::conformation::Residue&, unsigned long)+0xa0) [0x2aaaae10a9a0]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols_a.6.so(protocols::cyclic_peptide::PeptideStubMover::perform_single_iteration(core::pose::Pose&, core::chemical::ResidueTypeSet const&, unsigned long)+0x84) [0x2aaaae10b974]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols_a.6.so(protocols::cyclic_peptide::PeptideStubMover::apply(core::pose::Pose&)+0xb6) [0x2aaaae10ba86]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&)+0x22f) [0x2aaab375da3f]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_step(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&, bool)+0x1d) [0x2aaab375decd]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep, std::allocator<protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep> > >)+0x40) [0x2aaab375e580]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1ce) [0x2aaab3762d2e]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0x298d) [0x2aaab390031d]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x220) [0x2aaab39014a0]

/usr/local/apps/rosetta/2021.16_gcc-9.2.0_openmpi-4.0.5_1621611590/main/source/build/src/release/linux/3.10/64/x86/gcc/9.2/cxx11thread/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x43) [0x2aaab38e9613]

/usr/local/apps/rosetta/2021.16/bin/rosetta_scripts() [0x40483f]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaaba982445]

/usr/local/apps/rosetta/2021.16/bin/rosetta_scripts() [0x404a9b]

[END_BACKTRACE]

[FILE]: SIGSEGV

[LINE]: 11

[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]

[END_CRASH_REPORT]

 

very grateful for your time and help!

 

[Author]

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