############################################################################################################## # # Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/ # or use the script Rosetta/main/source/scripts/python/public/report_crashes.py # [START_CRASH_REPORT] [ROSETTA_VERSION]: 2020.08+release.cb1caba [COMMIT_DATE]: 2020-02-22T18:49:33.865989 [APPLICATION]: /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.mpi.linuxgccrelease [MODE]: Release [EXTRAS]: mpi (OpenMPI 4.0.5) [OS]: GNU/Linux [COMPILER]: GCC version "9.3.0" [STDLIB]: libstdc++ version 20200808 [START_OPTIONS] -in -in:file -in:file:s=PROT_LIG.pdb -in:file:extra_res_fa=COV.params -out -out:nstruct=20000 -out:prefix=ASx_ -out:file -out:file:scorefile=score_ASx.sc -run -run:ignore_zero_occupancy=false -parser -parser:protocol=dock.xml -jd2 -jd2:delete_old_poses -score -score:analytic_etable_evaluation -packing -packing:ex1 -packing:ex2 -mistakes -mistakes:restore_pre_talaris_2013_behavior -pH -pH:pH_mode -pH:value_pH=7.4 -qsar -qsar:grid_dir=qsar_grid -qsar:max_grid_cache_size=1 [END_OPTIONS] [START_BACKTRACE]: RAW_LIBC /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f8a07bb9eba] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x103) [0x7f8a07bb9583] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string, std::allocator > const&)+0x113) [0x7f8a07c7b0f3] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x3b) [0x7f8a07c7aebb] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libcore.2.so(core::conformation::check_good_cutpoint_neighbour(core::conformation::Residue const&, core::conformation::Residue const&)+0x174) [0x7f89ff242ce4] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libcore.2.so(core::conformation::update_cutpoint_virtual_atoms_if_connected(core::conformation::Conformation&, unsigned long, bool)+0x371) [0x7f89ff243111] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libcore.3.so(core::pose::add_variant_type_to_pose_residue(core::pose::Pose&, core::chemical::VariantType, unsigned long)+0x2e0) [0x7f8a00206830] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols_h.5.so(protocols::ligand_docking::MinimizeBackbone::add_cut_points(core::kinematics::Edge const&, protocols::ligand_docking::ligand_options::Interface const&, core::pose::Pose&)+0x328) [0x7f8a063da1c8] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols_h.5.so(protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(std::shared_ptr, protocols::ligand_docking::ligand_options::Interface const&, core::pose::Pose&)+0x24d5) [0x7f8a063e0305] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols_h.5.so(protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions(protocols::ligand_docking::ligand_options::Interface const&, core::pose::Pose&)+0x14e) [0x7f8a063e10fe] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols_h.5.so(protocols::ligand_docking::MinimizeBackbone::apply(core::pose::Pose&)+0x3a8) [0x7f8a063e34a8] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols_h.5.so(protocols::ligand_docking::FinalMinimizer::apply(core::pose::Pose&)+0x17d1) [0x7f8a0630b321] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x295) [0x7f8a08b15235] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator > >)+0x3b) [0x7f8a08b16a2b] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1ce) [0x7f8a08b176be] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x295) [0x7f8a08b15235] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator > >)+0x3b) [0x7f8a08b16a2b] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1ce) [0x7f8a08b176be] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x228d) [0x7f8a08ca56ad] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x23d) [0x7f8a08ca6f4d] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/mpi/libprotocols.1.so(protocols::jd2::MPIWorkPoolJobDistributor::go(std::shared_ptr)+0x320) [0x7f8a08ce4c50] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.mpi.linuxgccrelease(+0x284a) [0x56517dec184a] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f8a075190b3] /data/sam/sw/ROSETTA_3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.mpi.linuxgccrelease(+0x2b4e) [0x56517dec1b4e] [END_BACKTRACE] [FILE]: src/core/conformation/util.cc [LINE]: 654 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR: Error in core::conformation::check_good_cutpoint_neighbour(): The selected residue is neither an alpha-, beta-, or gamma-amino acid, nor a peptoid, nor a sugar, nor a nucleic acid, nor an oligourea. Nevertheless, it has a cutpoint variant type. This should not be possible. [END_MESSAGE] [END_CRASH_REPORT]