Abinitio doesn’t run but does not give output or error

This topic has 18 replies, 4 voices, and was last updated 7 years, 11 months ago by Anonymous.

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- October 28, 2016 at 5:04 pm #2529
  Anonymous
  I want to predict the structure of an 85 residue protein, but every time I run abinitio the program stops with no errors or structure output. The protein has a known structure, and I’ve run abinitio on it successfully. When I remove the .pdb file the output below is all I get. Any suggestions would be greatly appreciated.
  
  My input:
  
  ../../../main/source/bin/AbinitioRelax.default.macosgccrelease -in:file:fasta 3ccd.fasta -in:file:frag3 aat000_03_05.200_v1_3 -in:file:frag9 aat000_09_05.200_v1_3 -database ../../../main/database -abinitio:relax -nstruct 1 -out:pdb -out:path ./
  
  The output:
  
  core.init: Rosetta version exported from http://www.rosettacommons.org
  
  core.init: command: ../../../main/source/bin/AbinitioRelax.default.macosgccrelease -in:file:fasta 3ccd.fasta -in:file:frag3 aat000_03_05.200_v1_3 -in:file:frag9 aat000_09_05.200_v1_3 -database ../../../main/database -abinitio:relax -nstruct 1 -out:pdb -out:path ./
  
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1938315196 seed_offset=0 real_seed=1938315196
  
  core.init.random: RandomGenerator:init: Normal mode, seed=1938315196 RG_type=mt19937
  
  protocols.abinitio.AbrelaxApplication: read fasta sequence: 85 residues
  
  MFEQEVTITAPNGLDTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE
  
  protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
  
  core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1982 residue types
  
  core.io.fragments: reading fragments from file: aat000_09_05.200_v1_3 …
  
  core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
  
  core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file aat000_09_05.200_v1_3
  
  core.io.fragments: reading fragments from file: aat000_03_05.200_v1_3 …
  
  core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
  
  core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file aat000_03_05.200_v1_3
  
  core.fragment: compute strand/loop fractions for 85 residues…
  
  protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
  
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
  
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
  
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
  
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
  
  basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth
  
  basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
  
  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
  
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
  
  basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
  
  basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt
  
  basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt
  
  basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt
  
  basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt
  
  core.scoring: ATOM_VDW set to CENTROID_ROT
  
  core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
  
  basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
  
  core.scoring.CartesianBondedEnergy: Read 770 bb-independent lengths.
  
  basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
  
  core.scoring.CartesianBondedEnergy: Read 1464 bb-independent angles.
  
  basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
  
  core.scoring.CartesianBondedEnergy: Read 2110 bb-independent torsions.
  
  core.scoring: ATOM_VDW set to CENTROID_ROT
  
  protocols.jobdist.JobDistributors: S_00000001
  
  core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
  
  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.
  
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
  
  protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
  
  protocols::checkpoint: Deleting checkpoints of Abrelax
- October 31, 2016 at 5:55 pm #11935
  Anonymous
  How long does it take to fail? Instantly (it didn’t run the job) or slowly (it ran the job but the output went nowhere)?
  
  What does ‘When I remove the .pdb file the output below is all I get.’ mean? What pdb file?
- October 31, 2016 at 5:55 pm #12456
  Anonymous
  How long does it take to fail? Instantly (it didn’t run the job) or slowly (it ran the job but the output went nowhere)?
  
  What does ‘When I remove the .pdb file the output below is all I get.’ mean? What pdb file?
- October 31, 2016 at 5:55 pm #12977
  Anonymous
  How long does it take to fail? Instantly (it didn’t run the job) or slowly (it ran the job but the output went nowhere)?
  
  What does ‘When I remove the .pdb file the output below is all I get.’ mean? What pdb file?
- November 8, 2016 at 8:44 pm #11946
  Anonymous
  The job stops after about 5 seconds.
  
  What I mean about the pdb file is that I do not include it as part of the input. I want to be able to do the run on the sequence alone.
- November 8, 2016 at 8:44 pm #12467
  Anonymous
  The job stops after about 5 seconds.
  
  What I mean about the pdb file is that I do not include it as part of the input. I want to be able to do the run on the sequence alone.
- November 8, 2016 at 8:44 pm #12988
  Anonymous
  The job stops after about 5 seconds.
  
  What I mean about the pdb file is that I do not include it as part of the input. I want to be able to do the run on the sequence alone.
- November 8, 2016 at 9:55 pm #11947
  Anonymous
  Have you been through the tutorial? https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction
  
  What happens if you pass a non-existent fasta file? What happens if you put garbage IN the file? (The problem is that it apparently isn’t detecting the job from your fasta file).
  
  There’s probably something shallowly wrong with your options list, but since none of the people that use ab initio use the forums, we kind of have to guess where the problem is.
- November 8, 2016 at 9:55 pm #12468
  Anonymous
  Have you been through the tutorial? https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction
  
  What happens if you pass a non-existent fasta file? What happens if you put garbage IN the file? (The problem is that it apparently isn’t detecting the job from your fasta file).
  
  There’s probably something shallowly wrong with your options list, but since none of the people that use ab initio use the forums, we kind of have to guess where the problem is.
- November 8, 2016 at 9:55 pm #12989
  Anonymous
  Have you been through the tutorial? https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction
  
  What happens if you pass a non-existent fasta file? What happens if you put garbage IN the file? (The problem is that it apparently isn’t detecting the job from your fasta file).
  
  There’s probably something shallowly wrong with your options list, but since none of the people that use ab initio use the forums, we kind of have to guess where the problem is.
- November 14, 2016 at 11:21 pm #11961
  Anonymous
  Also take a look at the “Advanced” tutorial: https://www.rosettacommons.org/demos/latest/tutorials/advanced_denovo_structure_prediction/folding_tutorial
  
  It’s “advanced” only in the sense that it goes through things in more details, with a slightly different, more flexible protocol. You may have more luck using that approach.
- November 14, 2016 at 11:21 pm #12482
  Anonymous
  Also take a look at the “Advanced” tutorial: https://www.rosettacommons.org/demos/latest/tutorials/advanced_denovo_structure_prediction/folding_tutorial
  
  It’s “advanced” only in the sense that it goes through things in more details, with a slightly different, more flexible protocol. You may have more luck using that approach.
- November 14, 2016 at 11:21 pm #13003
  Anonymous
  Also take a look at the “Advanced” tutorial: https://www.rosettacommons.org/demos/latest/tutorials/advanced_denovo_structure_prediction/folding_tutorial
  
  It’s “advanced” only in the sense that it goes through things in more details, with a slightly different, more flexible protocol. You may have more luck using that approach.
- January 20, 2017 at 5:48 am #12105
  Anonymous
  I have a same problem with this guy. Please someone post the solution!
- January 20, 2017 at 5:48 am #12626
  Anonymous
  I have a same problem with this guy. Please someone post the solution!
- January 20, 2017 at 5:48 am #13147
  Anonymous
  I have a same problem with this guy. Please someone post the solution!
- January 23, 2017 at 4:52 pm #12113
  Anonymous
  To paraphrase Tolstoy, “Working Rosetta runs are all alike; every failing run is failing in its own way”
  
  It would be helpful to get more information about your particular run: what is your full commandline/option file, and could you describe the symptoms in your own way? (There might be additional information in how you describe things which might help diagnose your case.) — You may want to open a new forum thread for it, to keep things separate.
- January 23, 2017 at 4:52 pm #12634
  Anonymous
  To paraphrase Tolstoy, “Working Rosetta runs are all alike; every failing run is failing in its own way”
  
  It would be helpful to get more information about your particular run: what is your full commandline/option file, and could you describe the symptoms in your own way? (There might be additional information in how you describe things which might help diagnose your case.) — You may want to open a new forum thread for it, to keep things separate.
- January 23, 2017 at 4:52 pm #13155
  Anonymous
  To paraphrase Tolstoy, “Working Rosetta runs are all alike; every failing run is failing in its own way”
  
  It would be helpful to get more information about your particular run: what is your full commandline/option file, and could you describe the symptoms in your own way? (There might be additional information in how you describe things which might help diagnose your case.) — You may want to open a new forum thread for it, to keep things separate.
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