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

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

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
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
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.  Created 1982 residue types reading fragments from file: aat000_09_05.200_v1_3 ... rosetta++ fileformat detected! Calling legacy reader... 
core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file aat000_09_05.200_v1_3 reading fragments from file: aat000_03_05.200_v1_3 ... 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..... Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv Database file opened: scoring/score_functions/P_AA_pp/P_AA Database file opened: scoring/score_functions/P_AA_pp/P_AA_n Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt 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 Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 770 bb-independent lengths. Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1464 bb-independent angles. 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

Post Situation: 
Fri, 2016-10-28 10:04

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?

Mon, 2016-10-31 10:55

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.

Tue, 2016-11-08 12:44

Have you been through the tutorial?

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.

Tue, 2016-11-08 13:55

Also take a look at the "Advanced" 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.

Mon, 2016-11-14 15:21

I have a same problem with this guy. Please someone post the solution!

Thu, 2017-01-19 21:48

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.

Mon, 2017-01-23 08:52