Rosetta3.3 installation error

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    • October 26, 2011 at 3:40 pm #1069
      Anonymous

        Dear developers,

        I have downloaded Rosetta3.3 and run Scons bin mode=release. Everything seemed to be fine till I ran the tenzyme_design protocol.

        Here is what I got:

        /usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.3/rosetta_database/ @flags >first_try.log

        /usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

        I can find the liprprotocols.so file in one of the directories:

        /usr/local/rosetta3.3/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/libprotocols.so

        I understand that there was a problem with the database directory previously, and I had downloaded and installed the new database.tgz file.

        I had no trouble installing and running Rosetta3.2 previously. Did I miss something this time?

      • October 26, 2011 at 5:56 pm #6185
        Anonymous

          Weird. You haven’t done anything obviously wrong. I would suggest a wipe and reinstall:

          cd rosetta_source
          rm .sconsign.dblite
          rm bin/*
          rm -rf build/*
          scons.by bin mode=release

        • October 27, 2011 at 3:26 pm #6189
          Anonymous

            I followed your suggestion and reinstalled the program. Everything seems to be fine now. Many thanks for the help!

          • November 21, 2011 at 4:52 am #6284
            Anonymous

              I am trying to build the rosetta file by typing the commands : make gcc

              Here is the output coming………

              g++ -c -I. -Isrc -Iexternal/include -Isrc/platform/linux -Wall -W -pedantic -Wno-unused-variable -pipe -ffor-scope -fno-exceptions -malign-double -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -DNDEBUG -O3 -s -std=c++98 -MMD -MT .gcc.DirectedSimAnnealer.d -MF .gcc.DirectedSimAnnealer.d -MP DirectedSimAnnealer.cc -o .gcc.DirectedSimAnnealer.o
              In file included from src/utility/io/zipstream.hpp:651:0,
              from src/utility/io/izstream.hh:28,
              from src/utility/PeriodicSplineReader.hh:26,
              from ligand_ns.h:25,
              from DirectedSimAnnealer.cc:12:
              src/utility/io/zipstream.ipp: In member function ‘zlib_stream::basic_unzip_streambuf::int_type zlib_stream::basic_unzip_streambuf::underflow()’:
              src/utility/io/zipstream.ipp:427:26: error: ‘EOF’ was not declared in this scope
              src/utility/io/zipstream.ipp: In member function ‘int zlib_stream::basic_zip_istream::check_header()’:
              src/utility/io/zipstream.ipp:520:15: error: ‘EOF’ was not declared in this scope
              src/utility/io/zipstream.ipp:546:58: error: ‘EOF’ was not declared in this scope
              src/utility/io/zipstream.ipp:550:62: error: ‘EOF’ was not declared in this scope
              src/utility/io/zipstream.ipp:554:62: error: ‘EOF’ was not declared in this scope
              DirectedSimAnnealer.cc: In function ‘std::istream& pack::directed_design::operator>>(std::istream&, pack::directed_design::Entry&)’:
              DirectedSimAnnealer.cc:66:17: error: ‘INT_MAX’ was not declared in this scope
              DirectedSimAnnealer.cc: In member function ‘virtual void pack::DirectedSimAnnealer::run()’:
              DirectedSimAnnealer.cc:492:75: warning: suggest parentheses around ‘&&’ within ‘||’
              make: *** [.gcc.DirectedSimAnnealer.o] Error 1


              On typing the alternate command scons mode=release the result is

              scons: Reading SConscript files …

              scons: warning: The Options class is deprecated; use the Variables class instead.
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 32, in setup_build_options

              scons: warning: The EnumOption() function is deprecated; use the EnumVariable() function instead.
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 40, in setup_build_options

              scons: warning: The ListOption() function is deprecated; use the ListVariable() function instead.
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 48, in setup_build_options
              Traceback (most recent call last):
              File “/vcp1/people/gaurav/rosetta/rosetta++/SConstruct”, line 86, in main
              build = SConscript(“tools/build/setup.py”)
              File “/vcp1/people/gaurav/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 614, in __call__
              return method(*args, **kw)
              File “/vcp1/people/gaurav/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 551, in SConscript
              return _SConscript(self.fs, *files, **subst_kw)
              File “/vcp1/people/gaurav/lib/scons-2.1.0/SCons/Script/SConscript.py”, line 260, in _SConscript
              exec _file_ in call_stack[-1].globals
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 356, in
              build = setup()
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 347, in setup
              build.options_requested, build.options = setup_build_options()
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup.py”, line 95, in setup_build_options
              supported, actual.cxx, requested.cxx_ver
              File “/vcp1/people/gaurav/rosetta/rosetta++/tools/build/setup_platforms.py”, line 77, in select_compiler_version
              (actual, compiler)
              KeyError: “Unknown version number Linux) for compiler ‘gcc'”
              scons: done reading SConscript files.
              scons: Building targets …
              scons: `.’ is up to date.
              scons: done building targets.

              I am clueless after this and seek help to proceed further….I am currently using SUSE 11.3 and gcc version is 4.3.4 to install the rosetta.

            • November 21, 2011 at 11:58 pm #6292
              Anonymous

                Thanks lewis, I also tried with updating the basic.settings file but the outpur remains the same. Meanwhile I downloaded rosetta 3.3 and after untaring the bundle I have : ls
                Antibody-3.3.tgz foldit-3.3 new_apps.note README.Copyrights release.note rosetta3.3_demos.tgz rosetta3.3_manual.tgz
                BioTools-3.3.tgz foldit-3.3.tgz protocol_capture-3.3.tgz README.version rosetta3.3_database.tgz rosetta3.3_fragments.tgz rosetta3.3_source.tgz

                From rosetta_source tar file I have directory: ls
                accept_utracers.sh bin external lib performance-benchmark.py readme.txt SConscript SConstruct stubs test update_options.sh
                analysis build ide make_ctags.sh projects.settings rosetta_database scons.py src tags tools

                After that i have tried to build the file by scons bin command and there is several files installed in bin directory: ls
                AbinitioRelax.default.linuxgccdebug extract_atomtree_diffs.static.linuxgccrelease mpi_msd.static.linuxgccrelease
                AbinitioRelax.default.linuxgccrelease extract_pdbs.default.linuxgccdebug mr_protocols.default.linuxgccdebug
                AbinitioRelax.linuxgccdebug extract_pdbs.default.linuxgccrelease mr_protocols.default.linuxgccrelease
                AbinitioRelax.linuxgccrelease extract_pdbs.linuxgccdebug mr_protocols.linuxgccdebug
                AbinitioRelax.static.linuxgccdebug extract_pdbs.linuxgccrelease mr_protocols.linuxgccrelease
                AbinitioRelax.static.linuxgccrelease extract_pdbs.static.linuxgccrelease mr_protocols.static.linuxgccrelease
                AnchoredDesign.default.linuxgccdebug fix_alignment_to_match_pdb.default.linuxgccdebug pepspec_anchor_dock.default.linuxgccdebug
                AnchoredDesign.default.linuxgccrelease fix_alignment_to_match_pdb.default.linuxgccrelease pepspec_anchor_dock.default.linuxgccrelease
                AnchoredDesign.linuxgccdebug fix_alignment_to_match_pdb.linuxgccdebug pepspec_anchor_dock.linuxgccdebug
                AnchoredDesign.linuxgccrelease fix_alignment_to_match_pdb.linuxgccrelease pepspec_anchor_dock.linuxgccrelease
                AnchoredDesign.static.linuxgccdebug fix_alignment_to_match_pdb.static.linuxgccrelease pepspec_anchor_dock.static.linuxgccrelease
                AnchoredDesign.static.linuxgccrelease fixbb.default.linuxgccdebug pepspec.default.linuxgccdebug
                AnchoredPDBCreator.default.linuxgccdebug fixbb.default.linuxgccrelease pepspec.default.linuxgccrelease
                AnchoredPDBCreator.default.linuxgccrelease fixbb.linuxgccdebug pepspec.linuxgccdebug
                AnchoredPDBCreator.linuxgccdebug fixbb.linuxgccrelease pepspec.linuxgccrelease
                AnchoredPDBCreator.linuxgccrelease fixbb.static.linuxgccrelease pepspec.static.linuxgccrelease
                AnchoredPDBCreator.static.linuxgccdebug FlexPepDocking.default.linuxgccdebug relax.default.linuxgccdebug
                AnchoredPDBCreator.static.linuxgccrelease FlexPepDocking.default.linuxgccrelease relax.default.linuxgccrelease
                AnchorFinder.default.linuxgccdebug FlexPepDocking.linuxgccdebug relax.linuxgccdebug
                AnchorFinder.default.linuxgccrelease FlexPepDocking.linuxgccrelease relax.linuxgccrelease
                AnchorFinder.linuxgccdebug FlexPepDocking.static.linuxgccdebug relax.static.linuxgccrelease
                AnchorFinder.linuxgccrelease FlexPepDocking.static.linuxgccrelease revert_design_to_native.default.linuxgccdebug
                AnchorFinder.static.linuxgccdebug FloppyTail.default.linuxgccdebug revert_design_to_native.default.linuxgccrelease
                AnchorFinder.static.linuxgccrelease FloppyTail.default.linuxgccrelease revert_design_to_native.linuxgccdebug
                antibody_mode.default.linuxgccdebug FloppyTail.linuxgccdebug revert_design_to_native.linuxgccrelease
                antibody_mode.default.linuxgccrelease FloppyTail.linuxgccrelease revert_design_to_native.static.linuxgccrelease
                antibody_mode.linuxgccdebug FloppyTail.static.linuxgccdebug rna_database.default.linuxgccdebug
                antibody_mode.linuxgccrelease FloppyTail.static.linuxgccrelease rna_database.default.linuxgccrelease
                antibody_mode.static.linuxgccdebug fragment_picker.default.linuxgccdebug rna_database.linuxgccdebug
                antibody_mode.static.linuxgccrelease fragment_picker.default.linuxgccrelease rna_database.linuxgccrelease
                backrub.default.linuxgccdebug fragment_picker.linuxgccdebug rna_database.static.linuxgccrelease
                backrub.default.linuxgccrelease fragment_picker.linuxgccrelease rna_denovo.default.linuxgccdebug
                backrub.linuxgccdebug fragment_picker.static.linuxgccrelease rna_denovo.default.linuxgccrelease
                backrub.linuxgccrelease full_length_model.default.linuxgccdebug rna_denovo.linuxgccdebug
                backrub.static.linuxgccdebug full_length_model.default.linuxgccrelease rna_denovo.linuxgccrelease
                backrub.static.linuxgccrelease full_length_model.linuxgccdebug rna_denovo.static.linuxgccrelease
                benchmark.default.linuxgccdebug full_length_model.linuxgccrelease rna_design.default.linuxgccdebug
                benchmark.default.linuxgccrelease full_length_model.static.linuxgccrelease rna_design.default.linuxgccrelease
                benchmark.linuxgccdebug gen_apo_grids.default.linuxgccdebug rna_design.linuxgccdebug
                benchmark.linuxgccrelease gen_apo_grids.default.linuxgccrelease rna_design.linuxgccrelease
                benchmark.static.linuxgccdebug gen_apo_grids.linuxgccdebug rna_design.static.linuxgccrelease
                benchmark.static.linuxgccrelease gen_apo_grids.linuxgccrelease rna_extract.default.linuxgccdebug
                BuildPeptide.default.linuxgccdebug gen_apo_grids.static.linuxgccrelease rna_extract.default.linuxgccrelease
                BuildPeptide.default.linuxgccrelease gen_lig_grids.default.linuxgccdebug rna_extract.linuxgccdebug
                BuildPeptide.linuxgccdebug gen_lig_grids.default.linuxgccrelease rna_extract.linuxgccrelease
                BuildPeptide.linuxgccrelease gen_lig_grids.linuxgccdebug rna_extract.static.linuxgccrelease
                BuildPeptide.static.linuxgccdebug gen_lig_grids.linuxgccrelease rosettaDNA.default.linuxgccdebug
                BuildPeptide.static.linuxgccrelease gen_lig_grids.static.linuxgccrelease rosettaDNA.default.linuxgccrelease
                ca_to_allatom.default.linuxgccdebug idealize_jd2.default.linuxgccdebug rosettaDNA.linuxgccdebug
                ca_to_allatom.default.linuxgccrelease idealize_jd2.default.linuxgccrelease rosettaDNA.linuxgccrelease
                ca_to_allatom.linuxgccdebug idealize_jd2.linuxgccdebug rosettaDNA.static.linuxgccrelease
                ca_to_allatom.linuxgccrelease idealize_jd2.linuxgccrelease rosetta_scripts.default.linuxgccdebug
                ca_to_allatom.static.linuxgccrelease idealize_jd2.static.linuxgccrelease rosetta_scripts.default.linuxgccrelease
                cluster_alns.default.linuxgccdebug InterfaceAnalyzer.default.linuxgccdebug rosetta_scripts.linuxgccdebug
                cluster_alns.default.linuxgccrelease InterfaceAnalyzer.default.linuxgccrelease rosetta_scripts.linuxgccrelease
                cluster_alns.linuxgccdebug InterfaceAnalyzer.linuxgccdebug rosetta_scripts.static.linuxgccrelease
                cluster_alns.linuxgccrelease InterfaceAnalyzer.linuxgccrelease rotamer_recovery.default.linuxgccdebug
                cluster_alns.static.linuxgccrelease InterfaceAnalyzer.static.linuxgccdebug rotamer_recovery.default.linuxgccrelease
                cluster.default.linuxgccdebug InterfaceAnalyzer.static.linuxgccrelease rotamer_recovery.linuxgccdebug
                cluster.default.linuxgccrelease ligand_dock.default.linuxgccdebug rotamer_recovery.linuxgccrelease
                cluster.linuxgccdebug ligand_dock.default.linuxgccrelease rotamer_recovery.static.linuxgccrelease
                cluster.linuxgccrelease ligand_dock.linuxgccdebug score_aln2.default.linuxgccdebug
                cluster.static.linuxgccrelease ligand_dock.linuxgccrelease score_aln2.default.linuxgccrelease
                combine_silent.default.linuxgccdebug ligand_dock.static.linuxgccrelease score_aln2.linuxgccdebug
                combine_silent.default.linuxgccrelease ligand_rpkmin.default.linuxgccdebug score_aln2.linuxgccrelease
                combine_silent.linuxgccdebug ligand_rpkmin.default.linuxgccrelease score_aln2.static.linuxgccrelease
                combine_silent.linuxgccrelease ligand_rpkmin.linuxgccdebug score_aln.default.linuxgccdebug
                combine_silent.static.linuxgccrelease ligand_rpkmin.linuxgccrelease score_aln.default.linuxgccrelease
                CstfileToTheozymePDB.default.linuxgccdebug ligand_rpkmin.static.linuxgccrelease score_aln.linuxgccdebug
                CstfileToTheozymePDB.default.linuxgccrelease loopmodel.default.linuxgccdebug score_aln.linuxgccrelease
                CstfileToTheozymePDB.linuxgccdebug loopmodel.default.linuxgccrelease score_aln.static.linuxgccrelease
                CstfileToTheozymePDB.linuxgccrelease loopmodel.linuxgccdebug score.default.linuxgccdebug
                CstfileToTheozymePDB.static.linuxgccdebug loopmodel.linuxgccrelease score.default.linuxgccrelease
                CstfileToTheozymePDB.static.linuxgccrelease loopmodel.static.linuxgccrelease score_jd2.default.linuxgccdebug
                ddg_benchmark.default.linuxgccdebug loops_from_density.default.linuxgccdebug score_jd2.default.linuxgccrelease
                ddg_benchmark.default.linuxgccrelease loops_from_density.default.linuxgccrelease score_jd2.linuxgccdebug
                ddg_benchmark.linuxgccdebug loops_from_density.linuxgccdebug score_jd2.linuxgccrelease
                ddg_benchmark.linuxgccrelease loops_from_density.linuxgccrelease score_jd2.static.linuxgccrelease
                ddg_benchmark.static.linuxgccrelease loops_from_density.static.linuxgccrelease score.linuxgccdebug
                ddg_monomer.default.linuxgccdebug match.default.linuxgccdebug score.linuxgccrelease
                ddg_monomer.default.linuxgccrelease match.default.linuxgccrelease score.static.linuxgccrelease
                ddg_monomer.linuxgccdebug match.linuxgccdebug sequence_recovery.default.linuxgccdebug
                ddg_monomer.linuxgccrelease match.linuxgccrelease sequence_recovery.default.linuxgccrelease
                ddg_monomer.static.linuxgccrelease match.static.linuxgccrelease sequence_recovery.linuxgccdebug
                design_contrast_and_statistic.default.linuxgccdebug membrane_abinitio2.default.linuxgccdebug sequence_recovery.linuxgccrelease
                design_contrast_and_statistic.default.linuxgccrelease membrane_abinitio2.default.linuxgccrelease sequence_recovery.static.linuxgccrelease
                design_contrast_and_statistic.linuxgccdebug membrane_abinitio2.linuxgccdebug sequence_tolerance.default.linuxgccdebug
                design_contrast_and_statistic.linuxgccrelease membrane_abinitio2.linuxgccrelease sequence_tolerance.default.linuxgccrelease
                design_contrast_and_statistic.static.linuxgccrelease membrane_abinitio2.static.linuxgccrelease sequence_tolerance.linuxgccdebug
                docking_prepack_protocol.default.linuxgccdebug minimize_with_cst.default.linuxgccdebug sequence_tolerance.linuxgccrelease
                docking_prepack_protocol.default.linuxgccrelease minimize_with_cst.default.linuxgccrelease sequence_tolerance.static.linuxgccrelease
                docking_prepack_protocol.linuxgccdebug minimize_with_cst.linuxgccdebug super_aln.default.linuxgccdebug
                docking_prepack_protocol.linuxgccrelease minimize_with_cst.linuxgccrelease super_aln.default.linuxgccrelease
                docking_prepack_protocol.static.linuxgccrelease minimize_with_cst.static.linuxgccrelease super_aln.linuxgccdebug
                docking_protocol.default.linuxgccdebug minirosetta.default.linuxgccdebug super_aln.linuxgccrelease
                docking_protocol.default.linuxgccrelease minirosetta.default.linuxgccrelease super_aln.static.linuxgccrelease
                docking_protocol.linuxgccdebug minirosetta_graphics.default.linuxgccdebug SymDock.default.linuxgccdebug
                docking_protocol.linuxgccrelease minirosetta_graphics.default.linuxgccrelease SymDock.default.linuxgccrelease
                docking_protocol.static.linuxgccrelease minirosetta_graphics.linuxgccdebug SymDock.linuxgccdebug
                enzyme_design.default.linuxgccdebug minirosetta_graphics.linuxgccrelease SymDock.linuxgccrelease
                enzyme_design.default.linuxgccrelease minirosetta_graphics.static.linuxgccrelease SymDock.static.linuxgccdebug
                enzyme_design.linuxgccdebug minirosetta.linuxgccdebug SymDock.static.linuxgccrelease
                enzyme_design.linuxgccrelease minirosetta.linuxgccrelease UBQ_E2_thioester.default.linuxgccdebug
                enzyme_design.static.linuxgccrelease minirosetta.static.linuxgccrelease UBQ_E2_thioester.default.linuxgccrelease
                extract_atomtree_diffs.default.linuxgccdebug mpi_msd.default.linuxgccdebug UBQ_E2_thioester.linuxgccdebug
                extract_atomtree_diffs.default.linuxgccrelease mpi_msd.default.linuxgccrelease UBQ_E2_thioester.linuxgccrelease
                extract_atomtree_diffs.linuxgccdebug mpi_msd.linuxgccdebug UBQ_E2_thioester.static.linuxgccdebug
                extract_atomtree_diffs.linuxgccrelease mpi_msd.linuxgccrelease UBQ_E2_thioester.static.linuxgccrelease

                Now what would be the next step to be follwed to build the rosetta files. Please guide me as I am totally clueless to proceed…I even do not have any installation manual to follow.

              • November 23, 2011 at 5:44 am #6300
                Anonymous

                  Thanks, I am now try to run the Abinitio program from the rosetta_source directory while putting the flags as mention in the rosetta manual…got the following output:
                  ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb
                  core.init: Mini-Rosetta version Release 3.3, from SVN 42942 from https://svn.rosettacommons.org/source/branches/releases/rosetta-3.3/rose…
                  core.init: command: ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb
                  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1429852429 seed_offset=0 real_seed=1429852429
                  core.init.random: RandomGenerator:init: Normal mode, seed=1429852429 RG_type=mt19937
                  core.init: ROSETTA3_DB not defined
                  Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/

                  ERROR: Unable to open atomset file: ./chemical/atom_type_sets/fa_standard//atom_properties.txt
                  ERROR:: Exit from: src/core/chemical/AtomTypeSet.cc line: 88

                  While keeping the databse path in the command the result is:
                  ./bin/AbinitioRelax.linuxgccrelease -in:file:native -database rosetta_database 2RH1.pdb >test.pdb

                  ERROR: !pdb.empty()
                  ERROR:: Exit from: src/core/io/pdb/pdb_dynamic_reader.cc line: 212

                  What is the thing missing now??I am trying to run jobs from rosetta_source directory

                • November 24, 2011 at 5:07 am #6314
                  Anonymous

                    Hi Lewis,

                    I also tried runnig the score app zand found the following outputs:
                    ./bin/score.linuxgccrelease -in:file:s 1l2y.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/score.linuxgccrelease -in:file:s 1l2y.pdb -database rosetta_database/
                    core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1684117340 seed_offset=0 real_seed=-1684117340
                    core.init.random: RandomGenerator:init: Normal mode, seed=-1684117340 RG_type=mt19937

                    Rosetta Tool: score – rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files.
                    Usage:
                    PDB input: -in:file:s *.pdb or
                    -in:file:l list_of_pdbs
                    -no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
                    Silent input: -in:file:silent silent.out silent input filesname
                    -in:file:tags specify specific tags to be extracted, if left out all will be taken
                    -in:file:fullatom for full atom structures
                    -in:file:binary_silentfile for non-ideal structures (such as from looprelax)
                    -in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination)
                    -score_app:linmin Run a quick linmin before scoring
                    Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated)
                    Scorefunction: -score:weights weights weight set or weights file
                    -score:patch patch patch set
                    -score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch)
                    -score:optH_patch Weights patch file for optH
                    -rescore:verbose display score breakdown
                    Output: -out:nooutput don’t print PDB structures (default now)
                    -out:output force printing of PDB structures
                    -out:file:silent write silent-out file
                    -out:file:scorefile name write scorefile (default default.sc)
                    -out:prefix myprefix prefix the output structures with a string
                    Examples:
                    score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
                    Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally
                    it will print a PDB for every structure with -out:output flag

                    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.
                    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
                    protocols.jobdist.main: PDB Output Mode
                    protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1l2y.pdb 1
                    protocols.jobdist.main: Starting 1l2y_0001 …
                    core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types
                    core.import_pose.import_pose: PDB File:1l2y.pdb not found!

                    ERROR: Cannot open PDB file “1l2y.pdb”
                    ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 199

                     ./bin/score.linuxgccrelease -in:file:s 2RH1.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/score.linuxgccrelease -in:file:s 2RH1.pdb -database rosetta_database/
                    core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=34835792 seed_offset=0 real_seed=34835792
                    core.init.random: RandomGenerator:init: Normal mode, seed=34835792 RG_type=mt19937

                    Rosetta Tool: score – rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files.
                    Usage:
                    PDB input: -in:file:s *.pdb or
                    -in:file:l list_of_pdbs
                    -no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
                    Silent input: -in:file:silent silent.out silent input filesname
                    -in:file:tags specify specific tags to be extracted, if left out all will be taken
                    -in:file:fullatom for full atom structures
                    -in:file:binary_silentfile for non-ideal structures (such as from looprelax)
                    -in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination)
                    -score_app:linmin Run a quick linmin before scoring
                    Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated)
                    Scorefunction: -score:weights weights weight set or weights file
                    -score:patch patch patch set
                    -score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch)
                    -score:optH_patch Weights patch file for optH
                    -rescore:verbose display score breakdown
                    Output: -out:nooutput don’t print PDB structures (default now)
                    -out:output force printing of PDB structures
                    -out:file:silent write silent-out file
                    -out:file:scorefile name write scorefile (default default.sc)
                    -out:prefix myprefix prefix the output structures with a string
                    Examples:
                    score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
                    Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally
                    it will print a PDB for every structure with -out:output flag

                    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.
                    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
                    protocols.jobdist.main: PDB Output Mode
                    protocols.jobdist.JobDistributors: Looking for an available job: 1 1 2RH1.pdb 1
                    core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types

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

                    What could be the probable reason for this!!!!

                  • November 25, 2011 at 1:22 am #6321
                    Anonymous

                      I am able to run the score app while editing my existing file and the commands goes like this :
                      ./bin/score.linuxgccrelease -in:file:s 2RH1.pdb -database rosetta_database | egrep -v ‘Dunbrack library took .+ seconds to load’
                      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/score.linuxgccrelease -in:file:s 2RH1.pdb -database rosetta_database
                      core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1667183635 seed_offset=0 real_seed=-1667183635
                      core.init.random: RandomGenerator:init: Normal mode, seed=-1667183635 RG_type=mt19937

                      Rosetta Tool: score – rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files.
                      Usage:
                      PDB input: -in:file:s *.pdb or
                      -in:file:l list_of_pdbs
                      -no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
                      Silent input: -in:file:silent silent.out silent input filesname
                      -in:file:tags specify specific tags to be extracted, if left out all will be taken
                      -in:file:fullatom for full atom structures
                      -in:file:binary_silentfile for non-ideal structures (such as from looprelax)
                      -in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination)
                      -score_app:linmin Run a quick linmin before scoring
                      Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated)
                      Scorefunction: -score:weights weights weight set or weights file
                      -score:patch patch patch set
                      -score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch)
                      -score:optH_patch Weights patch file for optH
                      -rescore:verbose display score breakdown
                      Output: -out:nooutput don’t print PDB structures (default now)
                      -out:output force printing of PDB structures
                      -out:file:silent write silent-out file
                      -out:file:scorefile name write scorefile (default default.sc)
                      -out:prefix myprefix prefix the output structures with a string
                      Examples:
                      score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb
                      Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally
                      it will print a PDB for every structure with -out:output flag

                      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.
                      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
                      protocols.jobdist.main: PDB Output Mode
                      protocols.jobdist.JobDistributors: Looking for an available job: 1 1 2RH1.pdb 1
                      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
                      basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
                      Warning: Unable to locate database file Dunbrack02.lib.bin
                      Warning: Unable to locate database file Dunbrack02.lib.bin
                      Warning: Unable to locate database file Dunbrack02.lib.bin
                      core.pack.dunbrack: Opening file /tmp/dun02hVsFX4 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
                      protocols.jobdist.main: Starting 2RH1_0001 …
                      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
                      protocols.jobdist.main: Finished 2RH1_0001 in 1 seconds.
                      protocols.jobdist.main: Finished all 1 structures in 6 seconds.

                      There is a default.sc file has been created in the working directory, is that is the result file of this app? Where i can see the .pdb result file of this run.. if been created at all!!!

                    • February 24, 2012 at 12:48 pm #6688
                      Anonymous

                        after installtion how to run rosetta 3.3 software in linux?

                      • March 8, 2012 at 5:35 pm #6783
                        Anonymous

                          Can the executables be run from command line like a command by just typing “executable-name” without “./executable”. If so how? I have downloaded and installed rosetta3.3 in my home folder. My OS is Ubuntu 10.04.

                        • November 21, 2011 at 9:43 pm #6289
                          Anonymous

                            A) You appear to be building Rosetta++, meaning Rosetta2, not Rosetta3. I don’t support Rosetta2 but I’ll make my best guess.

                            B) Rosetta2 is ancient and the build system isn’t updated to know newer compilers/kernels/etc. Look for a file basic.settings, maybe basic.options (try tools/build/basic.options and basic.settings). Look for lists of GCC and linux kernel versions in these files. Update those lists to include your linux kernel version and gcc version as needed. Try compiling again from there. Good luck!

                          • November 22, 2011 at 2:39 am #6295
                            Anonymous

                              It looks ready to go. Use the (executable).linuxgccrelease commands for whatever rosetta stuff you want to do.

                            • November 23, 2011 at 4:54 pm #6303
                              Anonymous

                                ./bin/AbinitioRelax.linuxgccrelease -in:file:native -database rosetta_database 2RH1.pdb >test.pdb

                                A) You have mangled the order of the command line options. Each option’s argument needs to follow the option directly, like so:
                                ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.pdb -database rosetta_database

                                B) The > redirect won’t do what you appear to want. That is going to redirect the log file output to a file called “test.pdb”. I assume you are trying to put the result structure, not the log output, in a file. Rosetta will store output PDBs in automatically-named files (usually something like 2RH1_0001.pdb).

                                C) Abinitio relax will require more inputs than you are giving it (fragments files, etc http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_abinitio.html). If you want a simple test, run the score app instead; it requires no other inputs. If you want to learn what abrelax needs, read that document first.

                              • November 24, 2011 at 2:16 am #6310
                                Anonymous

                                  After follwing the instruction and points suggested by you I tried with following commands:
                                  ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.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 2RH1.pdb -database rosetta_database
                                  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-801851151 seed_offset=0 real_seed=-801851151
                                  core.init.random: RandomGenerator:init: Normal mode, seed=-801851151 RG_type=mt19937
                                  core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4218 residue types

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

                                  I have tried with another pdb file but the output is similar:
                                  /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=1386761343 seed_offset=0 real_seed=1386761343
                                  core.init.random: RandomGenerator:init: Normal mode, seed=1386761343 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

                                  I have also used the input the 1l2y.pdb file provided in the Abinitio/input directory but id diodn’t work too. One thing i found strange is that the pdb files in input directories are different from my pdb files and I am nt able to open the provided files.

                                  There is no output files folder and log folder i could find out in my Abinitio directory…..Do help me out to solve this puzzle!!!!

                                • November 24, 2011 at 2:45 am #6311
                                  Anonymous

                                    Rosetta needs a description of the chemical properties for each of the residues in the input pdb to do things like determine atom connectivity, atom properties, rotatable bonds, etc. The rosetta_database contains those descriptor files for all the standard amino acids and some others, but it doesn’t include all possible residues. Those errors are telling you that there is a residue which Rosetta doesn’t recognize in the pdb (i.e. MAL and NAG). There’s three ways to deal with this. One is to create a new parameter file for the residue (usually not done for things like glycosylation variants or adventitious ligands). The second is remove the offending residues from the input pdb. The third is to include the flag -ignore_unrecognized_res on the command line. Be careful with the last, as you may end up removing residues you didn’t intend to (which is why it’s not on by default).

                                    You’ll have to be more specific with 1l2y.pdb’s “it didn’t work”, as I doubt the unrecognized residue error is happening for the provided test file input. Regarding not being able to open it, integration/tests/abinitio/inputs/1l2y.pdb is not actually a pdb file (at least in the developers’ version), but rather a symlink to the 1l2y.pdb.gz file in the same directory. There’s some internal magic in Rosetta where it can often read gzipped files instead of the plain text version.

                                  • November 24, 2011 at 5:35 am #6315
                                    Anonymous

                                      Hi,

                                      I deleted the HETATM(which are probably unidentified by rosetta_database) and run the edited pdb file with and observed the following results:

                                      ./bin/AbinitioRelax.linuxgccrelease -in:file:native 2RH1.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 2RH1.pdb -database rosetta_database/
                                      core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1050352776 seed_offset=0 real_seed=-1050352776
                                      core.init.random: RandomGenerator:init: Normal mode, seed=-1050352776 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 3.29 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/dun02RdaYrG 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

                                      Is still there is something missing in the flag options….I am not able to see any output/log file for this run in my current working directory???

                                    • November 24, 2011 at 6:16 pm #6318
                                      Anonymous

                                        The “unrecognized aa MAL” is the same issue you were having before – the score application is no different from the abinitio application in this respect.

                                        The issue with 1l2y.pdb is likely the result of a difference between the applications, though. Where I said Rosetta “can often read gzipped files”, the “often” was put in deliberately, as there are annoyingly inconsistent cases where it can’t. Although I haven’t tested it, the score application may be one of those cases.

                                        Regarding the “inactive option accessed: -in:file:frag9”, you’re running up against Steven Lewis’s point C) – the abinitio application needs additional information (e.g. fragment files) to run properly.

                                      • November 25, 2011 at 1:30 am #6322
                                        Anonymous

                                          Score doesn’t give an output PDB unless specifically requested. All it does is score the input; since you already have the input and it isn’t modified, there’s no reason for it to output a PDB. score.sc is your scorefile containing the scores for the protein.

                                        • November 25, 2011 at 6:28 pm #6326
                                          Anonymous

                                            Note that you can force the score application to output a PDB by including the “-output” flag – This is covered in the documentation: http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_score_commands.html . This is useful if you want to see how Rosetta sees the structure (added hydrogens, repaired sidechains, omitted residues, etc.) without the complications of having a protocol modify the pose.

                                            P.S. The corresponding flag for score_jd2 application is -out:pdb

                                          • February 24, 2012 at 2:35 pm #6690
                                            Anonymous

                                              After you’ve compiled Rosetta, a bunch of symlinks to executables will show up in the rosetta_source/bin directory. They will look something like (application_name).(os)(compiler)(mode) – so, for example, fixbb.linuxgccrelease. These are your executables with which comprise Rosetta. They’re command line executables – you run them by typing them on the command line and then supplying a bunch of command line arguments to tell it what you want done.

                                              If you ask a more specific question I can give you a more specific answer.

                                            • March 8, 2012 at 7:03 pm #6787
                                              Anonymous

                                                This has nothing to do with Rosetta. Your $PATH environment variable needs to include the current directory to get this behavior.

                                                https://www.google.com/search?q=bash+include+current+directory+in+path

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