core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: /home/ubuntu/rosetta/main/source/bin/snugdock.linuxgccdebug -in:file:s ../../1_prepack/inputs/65plusCithFibA_fixedchains.prepack_flags2.pdb @flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-658793687 seed_offset=0 real_seed=-658793687 core.init.random: RandomGenerator:init: Normal mode, seed=-658793687 RG_type=mt19937 core.init: Resolved executable path: /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/snugdock.default.linuxgccdebug core.init: Looking for database based on location of executable: /home/ubuntu/rosetta/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed ../../1_prepack/inputs/65plusCithFibA_fixedchains.prepack_flags2.pdb nstruct indices 1 - 1000 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB ../../1_prepack/inputs/65plusCithFibA_fixedchains.prepack_flags2.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 416 residue types core.chemical.ResidueTypeSet: Total time to initialize 4.27 seconds. ERROR: Failed to apply a PatchOperation to CIT ERROR:: Exit from: src/core/chemical/Patch.cc line: 339 /home/ubuntu/rosetta/main/source/bin/snugdock.linuxgccdebug(print_backtrace(char const*)+0x3e) [0x4056bb] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x21f) [0x7f0b198c3b80] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::PatchCase::apply(core::chemical::ResidueType const&, bool) const+0x1d1) [0x7f0b0b25250b] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::Patch::apply(core::chemical::ResidueType const&, bool) const+0x118) [0x7f0b0b253c2e] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeSet::generate_residue_type(std::string const&) const+0x922) [0x7f0b0b333398] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeSet::name_mapOP(std::string const&) const+0x5a) [0x7f0b0b3329ec] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeSet::name_map(std::string const&) const+0x28) [0x7f0b0b33288e] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x6ab) [0x7f0b0b321c71] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1, std::allocator > > const&, unsigned long, bool) const+0x8f9) [0x7f0b0b321ebf] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::get_all_possible_residue_types(bool) const+0xbd) [0x7f0b0b320571] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.2.so(core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(utility::vector1 > const&)+0xb7) [0x7f0b0b320883] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(std::string const&, unsigned long, utility::vector1 > const&, std::string const&, bool, bool, bool, bool, bool, bool)+0x92f) [0x7f0b0d86572b] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x806) [0x7f0b0d8604ba] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x4b) [0x7f0b0d85e197] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.5.so(core::import_pose::build_pose_as_is(boost::shared_ptr, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xae) [0x7f0b0fd0966e] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.5.so(core::import_pose::build_pose(boost::shared_ptr, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0x69) [0x7f0b0fd0956e] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/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)+0x6f3) [0x7f0b0fd07736] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/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)+0xfd) [0x7f0b0fd07e2d] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x64) [0x7f0b0fd07cfa] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, boost::shared_ptr)+0x130) [0x7f0b1af641d2] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(boost::shared_ptr&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6ac) [0x7f0b1af333c2] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(boost::shared_ptr)+0xa2) [0x7f0b1af320ae] /home/ubuntu/rosetta/main/source/build/src/debug/linux/3.2/64/x86/gcc/4.6/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(boost::shared_ptr)+0x46) [0x7f0b1af0b934] /home/ubuntu/rosetta/main/source/bin/snugdock.linuxgccdebug() [0x4043c7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f0b185d176d] /home/ubuntu/rosetta/main/source/bin/snugdock.linuxgccdebug() [0x403ff9] Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '65plusCithFibA_fixedchains.prepack_flags2_0001' Error: [ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 339 ERROR: Failed to apply a PatchOperation to CIT 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: 65plusCithFibA_fixedchains.prepack_flags2_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1000 jobs considered, 1 jobs attempted in 9 seconds caught exception 1 jobs failed; check output for error messages