Disulfidize mover

Hello!

I want to scan all possible disulfides in a trimeric protein, but I haven’t been able to set up the  Disulfidize mover. Attached is my script. I get the following error:

protocols.denovo_design.DisulfidizeMover: building and scoring 494 to 1044

core.conformation.symmetry.Conformation: Add symmetric chemical bond 494 to 1044

core.conformation.symmetry.Conformation: Add symmetric chemical bond 940 to 152

core.conformation.symmetry.Conformation: Add symmetric chemical bond 48 to 598

protocols.toolbox.disulfide_util: [ ERROR ] Disulfide bond required between 48 and 152.

ERROR:: Exit from: src/core/util/disulfide_util.cc line: 165

BACKTRACE:

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2e6) [0x7fbc99a08596]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libcore.4.so(core::util::rebuild_disulfide(core::pose::Pose&, utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::shared_ptr<core::pack::task::PackerTask>, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::kinematics::MoveMap>, std::shared_ptr<core::scoring::ScoreFunction>)+0x260) [0x7fbc93773d30]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libcore.4.so(core::util::rebuild_disulfide(core::pose::Pose&, unsigned long, unsigned long, std::shared_ptr<core::pack::task::PackerTask>, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::kinematics::MoveMap>, std::shared_ptr<core::scoring::ScoreFunction>)+0x21e) [0x7fbc93776dae]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::make_disulfide(core::pose::Pose&, unsigned long, unsigned long, bool, std::shared_ptr<core::scoring::ScoreFunction>) const+0x34e) [0x7fbc8bfa1dbe]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide(core::pose::Pose&, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::scoring::ScoreFunction>, bool, unsigned long, unsigned long) const+0xda) [0x7fbc8bfa63ba]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::check_disulfide_score(core::pose::Pose&, unsigned long, unsigned long, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::scoring::ScoreFunction>) const+0x85) [0x7fbc8bfa65a5]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(core::pose::Pose const&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&, std::shared_ptr<core::scoring::ScoreFunction>) const+0x501) [0x7fbc8bfa6cd1]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(core::pose::Pose const&, utility::vector1<bool, std::allocator<bool> > const&, utility::vector1<bool, std::allocator<bool> > const&, std::shared_ptr<core::scoring::ScoreFunction>) const+0x314) [0x7fbc8bfa73f4]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols_a.6.so(protocols::denovo_design::DisulfidizeMover::process_pose(core::pose::Pose&, utility::vector1<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&)+0x2ba) [0x7fbc8bfa788a]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::MultiplePoseMover::process_poses(std::deque<std::shared_ptr<core::pose::Pose>, std::allocator<std::shared_ptr<core::pose::Pose> > >&)+0x1aa) [0x7fbc9ab5a33a]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::MultiplePoseMover::generate_pose()+0x175) [0x7fbc9ab5ea15]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::MultiplePoseMover::apply(core::pose::Pose&)+0x1b5d) [0x7fbc9ab6512d]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x29a) [0x7fbc9ab7759a]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x7fbc9ab7781b]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1c6) [0x7fbc9ab789f6]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7fbc9acfff4d]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x1bb) [0x7fbc9ad01dfb]

/home/karen/rosetta_2019.14.60699/main/source/build/src/release/linux/4.15/64/x86/gcc/7/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x56) [0x7fbc9ace8766]

/home/karen/rosetta_2019.14.60699/main/source/bin/rosetta_scripts.linuxgccrelease(+0x218e) [0x55cb5f23718e]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fbc98d7cb97]

/home/karen/rosetta_2019.14.60699/main/source/bin/rosetta_scripts.linuxgccrelease(+0x250a) [0x55cb5f23750a]

protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/util/disulfide_util.cc:165

[ ERROR ] UtilityExitException

ERROR:

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job INPUT_0002

File: src/core/util/disulfide_util.cc:165

[ ERROR ] UtilityExitException

ERROR:

protocols.jd2.JobDistributor: [ ERROR ]

protocols.jd2.JobDistributor: [ WARNING ] INPUT_0002 reported failure and will NOT retry

I would appreciate any help. Thank you very much for your time.

Best regards,

Karen Gonzalez