Reply To: about constraints

[Anonymous]

Hi, I changed the file name and did some further tests with crazy constraints, but it is still not crashed. It seems the constraints does not work properly. I do not know what’s wrong with it. Could you help me with it? Thank you very much! Here is the out file of Relax:

core.init: Mini-Rosetta version 40222:40309M from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.2/rosetta_source
core.init: command: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_source/bin/relax.linuxgccrelease -relax:fast -s ../pdb/MUFOLD-Server-T538_5.pdb -database /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database -out:pdb -constraints:cst_fa_file constraints_file_name -constraints:cst_fa_weight 10000000000000000 -out:nstruct 1 -out:prefix w
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1506506741 seed_offset=0 real_seed=-1506506741
core.init.random: RandomGenerator:init: Normal mode, seed=-1506506741 RG_type=mt19937
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
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.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/pdb_pair_stats_fine
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/P_AA
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/P_AA_n
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/P_AA_pp
core.io.database: Database file opened: /home/jiozhang/data/NIH/rosetta-3.2/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
protocols.relax.FastRelax: ================== Using default script ==================
core.scoring.constraints: Constraint choice: constraints_file_name
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushing ../pdb/MUFOLD-Server-T538_5.pdb nstruct index 1
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLN_p:CtermProteinFull 54
core.pack.task: Packer task: initialize from command line()
protocols.jd2.PDBJobInputter: filling pose from PDB ../pdb/MUFOLD-Server-T538_5.pdb
core.io.constraints: read constraints from constraints_file_name
core.pack.task: Packer task: initialize from command line()
core.scoring.dunbrack: Dunbrack library took 0.05 seconds to load from binary
protocols.relax.FastRelax: CMD: repeat 182.434 0 0 0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 624 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 464776 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -137.033 0.603466 0.603466 0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 578 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 436976 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -119.638 0.747985 0.747985 0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 547 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 380172 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -109.236 0.67832 0.67832 0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 549 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 371716 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -105.561 0.87336 0.87336 0.44
protocols.relax.FastRelax: MRP: 0 -105.561 -105.561 0.87336 0.87336
protocols.relax.FastRelax: CMD: accept_to_best -105.561 0.87336 0.87336 0.44
protocols.relax.FastRelax: CMD: endrepeat -105.561 0.87336 0.87336 0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 651 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 511620 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -155.431 1.06552 1.06552 0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 567 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 416428 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -127.201 0.881735 0.881735 0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 567 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 410624 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -116.007 0.876866 0.876866 0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 538 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 371416 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -106.84 0.906903 0.906903 0.44
protocols.relax.FastRelax: MRP: 1 -106.84 -106.84 0.906903 0.906903
protocols.relax.FastRelax: CMD: accept_to_best -106.84 0.906903 0.906903 0.44
protocols.relax.FastRelax: CMD: endrepeat -106.84 0.906903 0.906903 0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 655 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 520124 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -155.291 1.1129 1.1129 0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 559 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 411652 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -130.452 0.97148 0.97148 0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 557 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 398768 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -118.217 0.931387 0.931387 0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 549 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 383092 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -107.743 1.04338 1.04338 0.44
protocols.relax.FastRelax: MRP: 2 -107.743 -107.743 1.04338 1.04338
protocols.relax.FastRelax: CMD: accept_to_best -107.743 1.04338 1.04338 0.44
protocols.relax.FastRelax: CMD: endrepeat -107.743 1.04338 1.04338 0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 663 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 555524 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -152.422 1.1464 1.1464 0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 557 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 411004 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -131.224 1.03518 1.03518 0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 561 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 405632 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -119.508 1.03768 1.03768 0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 545 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 386024 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -108.762 1.0265 1.0265 0.44
protocols.relax.FastRelax: MRP: 3 -108.762 -108.762 1.0265 1.0265
protocols.relax.FastRelax: CMD: accept_to_best -108.762 1.0265 1.0265 0.44
protocols.relax.FastRelax: CMD: endrepeat -108.762 1.0265 1.0265 0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 662 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 544532 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -148.207 1.13287 1.13287 0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 574 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 415580 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -130.085 1.02975 1.02975 0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 561 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 388612 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -120.47 1.00552 1.00552 0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 549 rotamers at 54 positions.
core.pack.pack_rotamers: IG: 375220 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -109.946 1.03374 1.03374 0.44
protocols.relax.FastRelax: MRP: 4 -109.946 -109.946 1.03374 1.03374
protocols.relax.FastRelax: CMD: accept_to_best -109.946 1.03374 1.03374 0.44
protocols.relax.FastRelax: CMD: endrepeat -109.946 1.03374 1.03374 0.44
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.jd2.JobDistributor: wMUFOLD-Server-T538_5_0001 reported success in 13 seconds
protocols.jd2.JobDistributor: no more batches to process…
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 13 seconds
protocols::checkpoint: Deleting checkpoints of FastRelax