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Rosetta3.3 installation error

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Rosetta3.3 installation error
#1

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?

Post Situation: 
Wed, 2011-10-26 08:40
lzx32

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

Wed, 2011-10-26 10:56
smlewis

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

Thu, 2011-10-27 08:26
lzx32

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.

Sun, 2011-11-20 20:52
Gaurav_kumar

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!

Mon, 2011-11-21 13:43
smlewis

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.

Mon, 2011-11-21 15:58
Gaurav_kumar

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

Mon, 2011-11-21 18:39
smlewis

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

Tue, 2011-11-22 21:44
Gaurav_kumar

./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_...). 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.

Wed, 2011-11-23 08:54
smlewis

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/rose...
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/rose...
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!!!!

Wed, 2011-11-23 18:16
Gaurav_kumar

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.

Wed, 2011-11-23 18:45
rmoretti

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/rose...
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???

Wed, 2011-11-23 21:35
Gaurav_kumar

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/rose...
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/rose...
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!!!!

Wed, 2011-11-23 21:07
Gaurav_kumar

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.

Thu, 2011-11-24 10:16
rmoretti

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/rose...
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!!!

Thu, 2011-11-24 17:22
Gaurav_kumar

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.

Thu, 2011-11-24 17:30
smlewis

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_... . 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

Fri, 2011-11-25 10:28
rmoretti

after installtion how to run rosetta 3.3 software in linux?

Fri, 2012-02-24 04:48
kinjalpatel

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.

Fri, 2012-02-24 06:35
smlewis

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.

Thu, 2012-03-08 09:35
bhumika

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

Thu, 2012-03-08 11:03
smlewis