Runnig Abinitio & score app

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  • This topic has 9 replies, 2 voices, and was last updated 13 years ago by Anonymous.
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    • November 24, 2011 at 4:45 am #1100
      Anonymous

        I am new user of rosetta and still trying to figure out the commands and its function. I have installed rosetta3.3 on my suse 11.3 and now try to run the abintio application.The problem im facing is that i am not able to either pass on the flags/options in the command or may be doing it in incorrect manner.
        Can anyone help me to run two programs 1.AbinitioRelax.linuxgccrelease for which i used %(bin)s/minirosetta.%(binext)s @flags -database %(database)s -run:constant_seed -nodelay 2>&1 protocol
        The command goes like this:
        ./bin/AbinitioRelax.linuxgccrelease -in:file:native 1B9S.pdb -database rosetta_database/
        core.init: Mini-Rosetta version Release 3.3, from SVN 42942 from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.3/rosetta_source
        core.init: command: ./bin/AbinitioRelax.linuxgccrelease -in:file:native 1B9S.pdb -database rosetta_database/
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-362591609 seed_offset=0 real_seed=-362591609
        core.init.random: RandomGenerator:init: Normal mode, seed=-362591609 RG_type=mt19937
        core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types

        ERROR: unrecognized aa NAG
        ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 655

        Is it because I have not used -run:constant_seed -nodelay 2>&1 in the command line.

        How i can use this: test “${PIPESTATUS[0]}” != ‘0’ && exit 1 || true # for checking the executables from command line??

        I am also trying to run score app with it’s command protocol but failed to produce any output even.

        Any valuable suggestions??

      • November 24, 2011 at 6:50 pm #6320
        Anonymous

          While the integration test are a somewhat reasonable way of seeing how programs should be run, the machinery to get them to run in an automatic fashion confuses things somewhat. You may be better off reading the documentation for the application you hope to use, or by looking at the demos and tutorials, rather than the integration tests. (We just released a batch of new tutorials: http://www.rosettacommons.org/content/rosetta3-tutorials)

          The test “${PIPESTATUS[0]}” != ‘0’ && exit 1 || true is some Rosetta-independant bash magic so that the scripts work correctly in the integration test automated pipeline. If you’re launching the jobs manually, you don’t need it, and even if you are using a queuing system to run jobs, you should talk with your local cluster expert to set up a scheme that works with your queuing system.

          The 2>&1 is standard bash redirect specifications, should not affect how Rosetta runs, and is only worth including if you are redirecting the tracer output to a file. Rosetta doesn’t create a separate log file, but rather prints the logging information to standard out (and some error messages, if any, to standard error). It’s up to the user to redirect those to a file if they so desire.

          The -run:constant_seed flag simply tells Rosetta to use a constant seed for the pseudo-random number generator. This way the “random” numbers are consistent from test run to test run. With production runs you typically leave off that flag, as you want different runs to sample different trajectories.

          The -nodelay flag is typically superfluous, as it just tells Rosetta to skip staggering multiple runs with a random delay. The random delay is now off by default anyway, so the the -nodelay flag is just there for historical reasons and to override any delay setting that might accidently have gotten included in the flags file.

          The flags file is what your likely missing. That’s the “@flags” part of the command line. The @ symbol tells Rosetta to open the file specified ( “flags” in this case, but you can also use “@options.txt” to read options.txt, or “@../../my_super_abinitio.flags” to open the file “../../my_super_abinitio.flags”) and then read the flags specified there (one per line). In this way you don’t have to specify a dozen options on the command line, but can instead keep them in a file. (Documentation: http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/command_options.html)

        • November 25, 2011 at 5:21 am #6324
          Anonymous

            I have finally able to run the Abinitio commands and the output is as follows (although I have just used the given fragment files) :
            ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb -in:file:frag3 test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3 -database rosetta_database
            core.init: Mini-Rosetta version Release 3.3, from SVN 42942 from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.3/rosetta_source
            core.init: command: ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb -in:file:frag3 test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3 -database rosetta_database
            core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-2123604775 seed_offset=0 real_seed=-2123604775
            core.init.random: RandomGenerator:init: Normal mode, seed=-2123604775 RG_type=mt19937
            core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
            core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 442
            core.conformation.Conformation: Found disulfide between residues 78 163
            core.conformation.Conformation: current variant for 78 CYS
            core.conformation.Conformation: current variant for 163 CYS
            core.conformation.Conformation: current variant for 78 CYD
            core.conformation.Conformation: current variant for 163 CYD
            core.conformation.Conformation: Found disulfide between residues 156 162
            core.conformation.Conformation: current variant for 156 CYS
            core.conformation.Conformation: current variant for 162 CYS
            core.conformation.Conformation: current variant for 156 CYD
            core.conformation.Conformation: current variant for 162 CYD
            core.pack.task: Packer task: initialize from command line()
            core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
            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.
            basic.io.database: Database file opened: pdb_pair_stats_fine
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: CEN6_mem_env_log.txt
            basic.io.database: Database file opened: CEN10_mem_env_log.txt
            basic.io.database: Database file opened: memcbeta_den.txt
            basic.io.database: Database file opened: mem_pair_log.txt
            basic.io.database: Database file opened: P_AA
            basic.io.database: Database file opened: P_AA_n
            basic.io.database: Database file opened: P_AA_pp
            basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
            basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
            Warning: Unable to locate database file Dunbrack02.lib.bin
            core.pack.dunbrack: Dunbrack library took 2.59 seconds to load from ASCII
            Warning: Unable to locate database file Dunbrack02.lib.bin
            Warning: Unable to locate database file Dunbrack02.lib.bin
            core.pack.dunbrack: Opening file /tmp/dun02s6NrTV for output.
            core.pack.dunbrack: Moving temporary file to rosetta_database/Dunbrack02.lib.bin
            core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
            core.pack.pack_rotamers: built 7 rotamers at 1 positions.
            core.pack.pack_rotamers: IG: 476 bytes
            core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1202 residue types
            protocols.abinitio.AbrelaxApplication: take sequence from native : DEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL
            core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 442
            core.conformation.Conformation: Found disulfide between residues 78 163
            core.conformation.Conformation: current variant for 78 CYS
            core.conformation.Conformation: current variant for 163 CYS
            core.conformation.Conformation: current variant for 78 CYD
            core.conformation.Conformation: current variant for 163 CYD
            core.conformation.Conformation: Found disulfide between residues 156 162
            core.conformation.Conformation: current variant for 156 CYS
            core.conformation.Conformation: current variant for 162 CYS
            core.conformation.Conformation: current variant for 156 CYD
            core.conformation.Conformation: current variant for 162 CYD
            core.pack.task: Packer task: initialize from command line()
            core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
            core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
            core.pack.pack_rotamers: built 7 rotamers at 1 positions.
            core.pack.pack_rotamers: IG: 476 bytes
            ERROR: Value of inactive option accessed: -in:file:frag9
            ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb -in:file:frag3 test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3 -in:file:frag9 test/integration/tests/abinitio/inputs/aa1l2yA09_05.200_v1_3 -database rosetta_database
            core.init: Mini-Rosetta version Release 3.3, from SVN 42942 from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.3/rosetta_source
            core.init: command: ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb -in:file:frag3 test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3 -in:file:frag9 test/integration/tests/abinitio/inputs/aa1l2yA09_05.200_v1_3 -database rosetta_database
            core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1998302345 seed_offset=0 real_seed=1998302345
            core.init.random: RandomGenerator:init: Normal mode, seed=1998302345 RG_type=mt19937
            core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
            core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 442
            core.conformation.Conformation: Found disulfide between residues 78 163
            core.conformation.Conformation: current variant for 78 CYS
            core.conformation.Conformation: current variant for 163 CYS
            core.conformation.Conformation: current variant for 78 CYD
            core.conformation.Conformation: current variant for 163 CYD
            core.conformation.Conformation: Found disulfide between residues 156 162
            core.conformation.Conformation: current variant for 156 CYS
            core.conformation.Conformation: current variant for 162 CYS
            core.conformation.Conformation: current variant for 156 CYD
            core.conformation.Conformation: current variant for 162 CYD
            core.pack.task: Packer task: initialize from command line()
            core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
            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.
            basic.io.database: Database file opened: pdb_pair_stats_fine
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
            basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: CEN6_mem_env_log.txt
            basic.io.database: Database file opened: CEN10_mem_env_log.txt
            basic.io.database: Database file opened: memcbeta_den.txt
            basic.io.database: Database file opened: mem_pair_log.txt
            basic.io.database: Database file opened: P_AA
            basic.io.database: Database file opened: P_AA_n
            basic.io.database: Database file opened: P_AA_pp
            basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
            basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
            Warning: Unable to locate database file Dunbrack02.lib.bin
            core.pack.dunbrack: Dunbrack library took 2.17 seconds to load from ASCII
            Warning: Unable to locate database file Dunbrack02.lib.bin
            Warning: Unable to locate database file Dunbrack02.lib.bin
            core.pack.dunbrack: Opening file /tmp/dun02yzkR4x for output.
            core.pack.dunbrack: Moving temporary file to rosetta_database/Dunbrack02.lib.bin
            core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
            core.pack.pack_rotamers: built 7 rotamers at 1 positions.
            core.pack.pack_rotamers: IG: 476 bytes
            core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1202 residue types
            protocols.abinitio.AbrelaxApplication: take sequence from native : DEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCL
            core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP_p:NtermProteinFull 1
            core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU_p:CtermProteinFull 442
            core.conformation.Conformation: Found disulfide between residues 78 163
            core.conformation.Conformation: current variant for 78 CYS
            core.conformation.Conformation: current variant for 163 CYS
            core.conformation.Conformation: current variant for 78 CYD
            core.conformation.Conformation: current variant for 163 CYD
            core.conformation.Conformation: Found disulfide between residues 156 162
            core.conformation.Conformation: current variant for 156 CYS
            core.conformation.Conformation: current variant for 162 CYS
            core.conformation.Conformation: current variant for 156 CYD
            core.conformation.Conformation: current variant for 162 CYD
            core.pack.task: Packer task: initialize from command line()
            core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG
            core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
            core.pack.pack_rotamers: built 7 rotamers at 1 positions.
            core.pack.pack_rotamers: IG: 476 bytes
            core.io.fragments: reading fragments from file: test/integration/tests/abinitio/inputs/aa1l2yA09_05.200_v1_3 …
            core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
            core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file test/integration/tests/abinitio/inputs/aa1l2yA09_05.200_v1_3.gz
            core.io.fragments: reading fragments from file: test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3 …
            core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
            core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file test/integration/tests/abinitio/inputs/aa1l2yA03_05.200_v1_3.gz
            core.fragment: compute strand/loop fractions for 20 residues…
            protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
            basic.io.database: Database file opened: env_log.txt
            basic.io.database: Database file opened: cbeta_den.txt
            basic.io.database: Database file opened: pair_log.txt
            basic.io.database: Database file opened: cenpack_log.txt
            basic.io.database: Database file opened: phi.theta.36.HS.resmooth
            basic.io.database: Database file opened: phi.theta.36.SS.resmooth
            core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
            core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
            protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
            protocols.abinitio:
            ===================================================================
            Stage 1
            Folding with score0 for max of 2000
            protocols.abinitio: Replaced extended chain after 15 cycles.
            protocols.moves.MonteCarlo: ClassicFragmentM trials= 15; accepts= 0.9333; energy_drop/trial= 0.00000
            protocols.abinitio:

            Scores Weight Raw Score Wghtd.Score

            vdw 0.100 0.000 0.000

            Total weighted score: 0.000

            ===================================================================
            Stage 2
            Folding with score1 for 2000
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.moves.MonteCarlo: ClassicFragmentM trials= 2000; accepts= 0.2425; energy_drop/trial= -0.00377
            protocols.abinitio:

            Scores Weight Raw Score Wghtd.Score

            vdw 1.000 0.000 0.000
            pair 1.000 -2.768 -2.768
            env 1.000 301.627 301.627
            hs_pair 1.000 0.000 0.000
            ss_pair 0.300 0.000 0.000
            sheet 1.000 0.000 0.000

            Total weighted score: 298.859

            ===================================================================
            Stage 3
            Folding with score2 and score5 for 2000
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.abinitio: stop cycles in stage3 due to convergence
            protocols.moves.MonteCarlo: ClassicFragmentM trials= 397; accepts= 0.2166; energy_drop/trial= 0.00658
            protocols.abinitio:

            Scores Weight Raw Score Wghtd.Score

            vdw 1.000 0.000 0.000
            cenpack 0.500 -3.089 -1.545
            pair 1.000 -1.246 -1.246
            env 1.000 301.089 301.089
            cbeta 0.250 258.868 64.717
            hs_pair 1.000 0.000 0.000
            ss_pair 1.000 0.000 0.000
            sheet 1.000 0.000 0.000

            Total weighted score: 363.015

            ===================================================================
            Stage 4
            Folding with score3 for 4000
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.moves.MonteCarlo: autotemp_reject — heat: 150 2
            protocols.moves.MonteCarlo: autotemp_accept: reset temperature_ = 2
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.basic_moves.FragmentMover: couldn’t find fragment to insert!!
            protocols.moves.MonteCarlo: ClassicFragmentM trials= 4000; accepts= 0.3115; energy_drop/trial= 0.00251
            protocols.moves.MonteCarlo: SmoothFragmentMo trials= 8000; accepts= 0.3728; energy_drop/trial= 0.00515
            protocols.abinitio:

            Scores Weight Raw Score Wghtd.Score

            vdw 1.000 0.566 0.566
            cenpack 1.000 -4.111 -4.111
            pair 1.000 0.483 0.483
            env 1.000 296.089 296.089
            cbeta 1.000 258.129 258.129
            rg 3.000 451.351 1354.053
            hs_pair 1.000 0.000 0.000
            ss_pair 1.000 0.000 0.000
            rsigma 1.000 0.000 0.000
            sheet 1.000 0.000 0.000

            Total weighted score: 1905.208

            ===================================================================
            Finished Abinitio

            protocols.abinitio.AbrelaxApplication: Finished _0001 in 58 seconds.
            protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
            protocols::checkpoint: Deleting checkpoints of Abrelax
            protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
            protocols::checkpoint: Deleting checkpoints of Abrelax

            I have observed few scoring tables in the run ouput:
            1. Is these score were the result of this succesful run( I am not sure of that)?
            2. Where is the default result file is generated out of this abinitio app (I couldn’t see any in my working directory)?
            3. How to interpret the full atom score file?

            Your help is solicited!!!!

          • December 1, 2011 at 4:50 am #6352
            Anonymous

              I am able to run the Abinitio application and able to generate the output files. I am wandering how to proceed further and even not get any clue even from the “Post processing” thing. I am sending you the command which i used to generate the “.out” files and the generated file as an attachement!!!
              Please guide me how to interpret the file values and take the same for the further analysis, I want to do analyses the structure prediction of my given proteins.

              command: ./bin/AbinitioRelax.linuxgccrelease -in:file:native ../demos/membrane_abinitio/rosetta_inputs/BRD4.pdb -in:file:frag3 ../demos/membrane_abinitio/rosetta_inputs/aaBRD4_03_05.200_v1_3 -in:file:frag9 ../demos/membrane_abinitio/rosetta_inputs/aaBRD4_09_05.200_v1_3 -database rosetta_database -abinitio:relax -nstruct 1 -out:file:silent BRD.out

            • December 8, 2011 at 4:37 am #6375
              Anonymous

                Can you please let me know how to submit/run my protein files for abinitio and relax process in multiple processor??

                Please write the full command so that it would be easier for me to follow the same!!!

              • December 8, 2011 at 9:38 pm #6379
                Anonymous

                  From the abinitio documentation (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_abinitio.html):

                  The standard command line for optimal performance is shown below (nstruct should be set depending on how many models you want to generate):

                  ../../bin/AbinitioRelax.linuxgccrelease
                  -database ../../rosetta_database
                  -in:file:fasta ./input_files/1elwA.fasta
                  -in:file:native ./input_files/1elw.pdb
                  -in:file:frag3 ./input_files/aa1elwA03_05.200_v1_3
                  -in:file:frag9 ./input_files/aa1elwA09_05.200_v1_3
                  -abinitio:relax
                  -relax:fast
                  -abinitio::increase_cycles 10
                  -abinitio::rg_reweight 0.5
                  -abinitio::rsd_wt_helix 0.5
                  -abinitio::rsd_wt_loop 0.5
                  -use_filters true
                  -psipred_ss2 ./input_files/1elwA.psipred_ss2
                  -kill_hairpins ./input_files/1elwA.psipred_ss2
                  -out:file:silent 1elwA_silent.out
                  -nstruct 10

                  Note that you will have to change the filenames, paths, and possibly other options according to your own situation.

                  As far as I’m aware, the AbinitioRelax application is trivially parallel – i.e. to run it on multiple processors, all you have to do is launch the application multiple times (with different output directories so that they don’t overwrite each other).

                  The one possible tricky bit is that if all the processes start at the same time (within the same second), the pseudorandom number generator won’t be different for each, and you’ll get repeated results. If this would be a concern, I’d give the -seed_offset option a different value for each run. (Or you can explicitly set the seed with -constant_seed & -jran — all of this is discussed in the Abinitio documentation.)

                • November 25, 2011 at 6:58 pm #6329
                  Anonymous

                    I haven’t done abinitio myself, so I’m not too clear on the particulars, but the abinitio documentation (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_abinitio.html) has a section on “Post Processing” which should give pointers on where to go next.

                  • December 1, 2011 at 7:56 pm #6353
                    Anonymous

                      The big question is what is the overall goal you wish to accomplish, and what additional information you have that you can bring to bear on the problem.

                      As the Post Processing section notes, a likely first step is to run the cluster application on your results (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_cluster.html). The most native-like structure is likely to be in a large cluster with many low total energy structures.

                      You can also use other information to help guide model selection – conserved regions will likely show a structural reason for conservation. If there are known active site residues, they’ll likely cluster in a single active site or an interaction surface.

                      You may find additional helpful information in the recently released Rosetta tutorials (See http://www.rosettacommons.org/content/rosetta3-tutorials), or the workshops and presentations the Meiler Lab put together (See the Movies and Rosetta Tutorials tabs at http://www.meilerlab.org/index.php/jobs/resources)

                    • December 8, 2011 at 11:50 pm #6382
                      Anonymous

                        Thanks for the information. I want to precisely run my jobs in parallel on different machines of the network or in more than one processor of my local machine (6 processor). I need to know the commands/process to assign the jobs for this and how we can compile the results file in that case??

                      • December 9, 2011 at 2:10 am #6386
                        Anonymous

                          I’d talk with your local sysadmin/cluster guru to figure out the preferred way to launch jobs on your system – they may have a preferred job distribution system in use. If not, you can possibly just write a shell script which will launch the jobs (or simply launch them manually).

                          Regarding compiling the results, the typical output of the AbinitioRelax application is a Rosetta silent file. In most cases, multiple silent files can simply be concatenated together to get a single silent file (e.g. “cat rundir*/1elwA_silent.out > 1e1wA_combined.out”).

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