I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:
#!/bin/bash
$ROSETTA3/source/bin/rosetta_scripts.linuxgccrelease \
-in::file::s /home/labusr/Documents/tubulin_PF_dep_noligand.pdb\
-parser::protocol /home/labusr/Documents/A_asymm_refine.xml \
-parser::script_vars denswt=35 rms=1.5 reso=4.3 map=/home/labusr/Documents/tublin_map_masked.mrc testmap=/home/labusr/Documents/tubulin_test_map_right.mrc
-ignore_unrecognized_res \
-edensity::mapreso 4.3 \
-default_max_cycles 200 \
-edensity::cryoem_scatterers \
-beta \
-out::suffix _$1 \
-crystal_refine
Even though I'm using the flag -ignore_unrecognized_res, I'm getting this error here:
BACKTRACE: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7f7a7576948f] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > > const&)+0x5b1) [0x7f7a785053c1] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&)+0xe1) [0x7f7a7850e3a1] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x472) [0x7f7a7850f2a2] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x30) [0x7f7a78510720] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose_as_is(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xc3) [0x7f7a79c06383] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xab) [0x7f7a79c0682b] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x552) [0x7f7a79c0b392] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7f7a79c0c330] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7f7a79c0c51b] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7f7a7a64dd75] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7f7a7a62805a] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7f7a7a629f71] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7f7a7a6016ba] /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f7a7375ec05] /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b] ./Tublin_exercise_refine.sh: line 8: -in:ignore_unrecognized_res: command not found core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org core.init: command: /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease -in::file::s /home/labusr/Documents/tubulin_PF_dep_final.pdb -parser::protocol /home/labusr/Documents/A_asymm_refine.xml -parser::script_vars denswt=35 rms=1.5 reso=4.3 map=/home/labusr/Documents/tublin_map_masked.mrc testmap=/home/labusr/Documents/tubulin_test_map_right.mrc core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1356985856 seed_offset=0 real_seed=1356985856 core.init.random: RandomGenerator:init: Normal mode, seed=1356985856 RG_type=mt19937 core.init: Resolved executable path: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/rosetta_scripts.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/labusr/rosetta/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /home/labusr/Documents/tubulin_PF_dep_final.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /home/labusr/Documents/tubulin_PF_dep_final.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 557 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.61 seconds. core.import_pose.import_pose: File '/home/labusr/Documents/tubulin_PF_dep_final.pdb' automatically determined to be of type PDB Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'tubulin_PF_dep_final_0001' Error: [ ERROR ] [ ERROR ] EXCN_utility_exit has been thrown from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1217 ERROR: Unrecognized residue: GTP Error: [ ERROR ] Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: tubulin_PF_dep_final_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages Error: [ ERROR ] ERROR: Unrecognized residue: GTP ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1217 BACKTRACE: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7fd3c412b48f] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > > const&)+0x5b1) [0x7fd3c6ec73c1] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&)+0xe1) [0x7fd3c6ed03a1] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x472) [0x7fd3c6ed12a2] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x30) [0x7fd3c6ed2720] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose_as_is(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xc3) [0x7fd3c85c8383] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xab) [0x7fd3c85c882b] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x552) [0x7fd3c85cd392] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7fd3c85ce330] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7fd3c85ce51b] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7fd3c900fd75] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7fd3c8fea05a] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7fd3c8febf71] /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7fd3c8fc36ba] /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd3c2120c05] /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b] ./Tublin_exercise_refine.sh: line 8: -in:ignore_unrecognized_res: command not found
Category:
Post Situation:
Each line needs to end with a \ in your bash script otherwise the flags after it won't be read. Make sure the line that starts with -parser_script_vars is on the same line that has testmap=... and then put a "\" at the end of the line. That should resolve the issue.
Thanks. It works now. I did try the script on the structure after removing the ligand. I got an error related to the density. You can find more details here: https://www.rosettacommons.org/node/10118. Cheers.