Error with -patch_selectors – Rosetta Commons

This topic has 12 replies, 2 voices, and was last updated 7 years, 7 months ago by Anonymous.

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- June 6, 2017 at 9:40 pm #2667
  Anonymous
  HI there,
  
  I am trying to predict the structure of a protein which has some diordered regions in it. I found a paper that performed the modeling of a protein with disordered regions by considering the disordered region as -replonly. So, I am trying to use the same approach, but ended up with the below error.
  
  [ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 349
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  Can anybody help me understand what it is and how to fix it?
  
  Commands:
  
  AbinitioRelax.default.macosclangrelease -in:file:fasta ./c2.fasta
  
  -in:file:frag3 ./aat000_03_05.200_v1_3.txt
  
  -in:file:frag9 ./aat000_09_05.200_v1_3.txt
  
  -database $MYPATH/main/database –
  
  abinitio:relax
  
  -nstruct 100
  
  -out:pdb
  
  -use_filters true
  
  -psipred_ss2 ./t000_.psipred_ss2.txt
  
  -abinitio::increase_cycles 10
  
  -replonly_residues 65 70 71 72 73 74 75 76 77 78 79 80 81 92 93 94 95 96 101 102 103 104 105 106 107 108 109 110 111 112 113 125 126 127 128 129 130 131 138 139 150 151 152 153 155 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 207 209 210 215 216 217 218 219 220 221 222 223 224 225 226
  
  -correct
  
  -patch_selectors replonly
- June 6, 2017 at 10:08 pm #12378
  Anonymous
  It would seem CYZ and REPLONLY aren’t intercompatible.
  
  There is probably a “correct fix” but I don’t know what it is.
  
  The easy fix is to comment out CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt. CYZ is used for chemical conjugations through cysteine sidechains (CYS is for free cysteine, and CYD for disulfide) – you don’t need it. If other residue types hit this problem – the same hack is likely to work, assuming you don’t turn off one of the important ones. Assuming you are working with a protein with only canonical residues, feel safe throwing out anything that isn’t a canonical amino acid from that file. Be sure to turn them back on before you try a different project, though.
- June 6, 2017 at 10:08 pm #12899
  Anonymous
  It would seem CYZ and REPLONLY aren’t intercompatible.
  
  There is probably a “correct fix” but I don’t know what it is.
  
  The easy fix is to comment out CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt. CYZ is used for chemical conjugations through cysteine sidechains (CYS is for free cysteine, and CYD for disulfide) – you don’t need it. If other residue types hit this problem – the same hack is likely to work, assuming you don’t turn off one of the important ones. Assuming you are working with a protein with only canonical residues, feel safe throwing out anything that isn’t a canonical amino acid from that file. Be sure to turn them back on before you try a different project, though.
- June 6, 2017 at 10:08 pm #13420
  Anonymous
  It would seem CYZ and REPLONLY aren’t intercompatible.
  
  There is probably a “correct fix” but I don’t know what it is.
  
  The easy fix is to comment out CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt. CYZ is used for chemical conjugations through cysteine sidechains (CYS is for free cysteine, and CYD for disulfide) – you don’t need it. If other residue types hit this problem – the same hack is likely to work, assuming you don’t turn off one of the important ones. Assuming you are working with a protein with only canonical residues, feel safe throwing out anything that isn’t a canonical amino acid from that file. Be sure to turn them back on before you try a different project, though.
- June 8, 2017 at 5:33 pm #12386
  Anonymous
  Thanks very much for the kind reply.
  
  I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt and got the same error. So, I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt.slim
  
  and still getting similar error:
  
  *************
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  ERROR:: Exit from: src/core/chemical/Patch.cc line: 349
  
  0 libutility.dylib 0x000000010cb39a1b print_backtrace(char const*) + 59
  
  1 libutility.dylib 0x000000010cb39847 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 887
  
  2 libcore.2.dylib 0x000000010bfc6f40 core::chemical::PatchCase::apply(core::chemical::ResidueType const&, bool) const + 448
  
  3 libcore.2.dylib 0x000000010bfc8889 core::chemical::Patch::apply(core::chemical::ResidueType const&, bool) const + 265
  
  4 libcore.2.dylib 0x000000010c063711 core::chemical::ResidueTypeSet::generate_residue_type(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 2033
  
  5 libcore.2.dylib 0x000000010c062e9a core::chemical::ResidueTypeSet::name_mapOP(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 74
  
  6 libcore.2.dylib 0x000000010c062d23 core::chemical::ResidueTypeSet::name_map(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 35
  
  7 libcore.2.dylib 0x000000010c056fd2 core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 1794
  
  8 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  9 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  10 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  11 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  12 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  13 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  14 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  15 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  16 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  17 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  18 libcore.2.dylib 0x000000010c058ff8 core::chemical::ResidueTypeFinder::get_all_possible_residue_types(bool) const + 280
  
  19 libcore.2.dylib 0x000000010c06a4b4 core::chemical::ResidueTypeSetCache::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) + 852
  
  20 libcore.2.dylib 0x000000010bfb6bd3 core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) const + 67
  
  21 libcore.4.dylib 0x000000010a0872db core::pack::task::ResidueLevelTask_::ResidueLevelTask_(core::conformation::Residue const&, core::pose::Pose const&) + 859
  
  22 libcore.4.dylib 0x000000010a07f269 core::pack::task::PackerTask_::PackerTask_(core::pose::Pose const&) + 489
  
  23 libcore.4.dylib 0x000000010a0a05e8 core::pack::task::TaskFactory::create_packer_task(core::pose::Pose const&) + 40
  
  24 libprotocols_b.5.dylib 0x0000000105c569ce protocols::abinitio::ResolutionSwitcher::apply(core::pose::Pose&) + 1230
  
  25 libprotocols_b.5.dylib 0x0000000105b903c4 protocols::abinitio::AbrelaxApplication::fold(core::pose::Pose&, std::__1::shared_ptr<protocols::abinitio::Protocol>) + 7748
  
  26 libprotocols_b.5.dylib 0x0000000105b92eef protocols::abinitio::AbrelaxApplication::run() + 351
  
  27 AbinitioRelax.default.macosclangrelease 0x00000001043fd655 main + 501
  
  28 libdyld.dylib 0x00007fff938585ad start + 1
  
  29 ??? 0x0000000000000085 0x0 + 133
  
  Error: Must call shutdown() when finished using job distributor!
  
  protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
  
  Exception :
  
  [ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 349
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  **********
  
  I would really appreciate any help to solve this.
  
  Thanks,
  
  Subha
- June 8, 2017 at 5:33 pm #12907
  Anonymous
  Thanks very much for the kind reply.
  
  I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt and got the same error. So, I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt.slim
  
  and still getting similar error:
  
  *************
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  ERROR:: Exit from: src/core/chemical/Patch.cc line: 349
  
  0 libutility.dylib 0x000000010cb39a1b print_backtrace(char const*) + 59
  
  1 libutility.dylib 0x000000010cb39847 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 887
  
  2 libcore.2.dylib 0x000000010bfc6f40 core::chemical::PatchCase::apply(core::chemical::ResidueType const&, bool) const + 448
  
  3 libcore.2.dylib 0x000000010bfc8889 core::chemical::Patch::apply(core::chemical::ResidueType const&, bool) const + 265
  
  4 libcore.2.dylib 0x000000010c063711 core::chemical::ResidueTypeSet::generate_residue_type(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 2033
  
  5 libcore.2.dylib 0x000000010c062e9a core::chemical::ResidueTypeSet::name_mapOP(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 74
  
  6 libcore.2.dylib 0x000000010c062d23 core::chemical::ResidueTypeSet::name_map(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 35
  
  7 libcore.2.dylib 0x000000010c056fd2 core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 1794
  
  8 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  9 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  10 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  11 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  12 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  13 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  14 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  15 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  16 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  17 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  18 libcore.2.dylib 0x000000010c058ff8 core::chemical::ResidueTypeFinder::get_all_possible_residue_types(bool) const + 280
  
  19 libcore.2.dylib 0x000000010c06a4b4 core::chemical::ResidueTypeSetCache::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) + 852
  
  20 libcore.2.dylib 0x000000010bfb6bd3 core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) const + 67
  
  21 libcore.4.dylib 0x000000010a0872db core::pack::task::ResidueLevelTask_::ResidueLevelTask_(core::conformation::Residue const&, core::pose::Pose const&) + 859
  
  22 libcore.4.dylib 0x000000010a07f269 core::pack::task::PackerTask_::PackerTask_(core::pose::Pose const&) + 489
  
  23 libcore.4.dylib 0x000000010a0a05e8 core::pack::task::TaskFactory::create_packer_task(core::pose::Pose const&) + 40
  
  24 libprotocols_b.5.dylib 0x0000000105c569ce protocols::abinitio::ResolutionSwitcher::apply(core::pose::Pose&) + 1230
  
  25 libprotocols_b.5.dylib 0x0000000105b903c4 protocols::abinitio::AbrelaxApplication::fold(core::pose::Pose&, std::__1::shared_ptr<protocols::abinitio::Protocol>) + 7748
  
  26 libprotocols_b.5.dylib 0x0000000105b92eef protocols::abinitio::AbrelaxApplication::run() + 351
  
  27 AbinitioRelax.default.macosclangrelease 0x00000001043fd655 main + 501
  
  28 libdyld.dylib 0x00007fff938585ad start + 1
  
  29 ??? 0x0000000000000085 0x0 + 133
  
  Error: Must call shutdown() when finished using job distributor!
  
  protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
  
  Exception :
  
  [ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 349
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  **********
  
  I would really appreciate any help to solve this.
  
  Thanks,
  
  Subha
- June 8, 2017 at 5:33 pm #13428
  Anonymous
  Thanks very much for the kind reply.
  
  I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt and got the same error. So, I tried commenting out the CYZ from database/chemical/residue_type_sets/fa_standard/residue_types.txt.slim
  
  and still getting similar error:
  
  *************
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  ERROR:: Exit from: src/core/chemical/Patch.cc line: 349
  
  0 libutility.dylib 0x000000010cb39a1b print_backtrace(char const*) + 59
  
  1 libutility.dylib 0x000000010cb39847 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 887
  
  2 libcore.2.dylib 0x000000010bfc6f40 core::chemical::PatchCase::apply(core::chemical::ResidueType const&, bool) const + 448
  
  3 libcore.2.dylib 0x000000010bfc8889 core::chemical::Patch::apply(core::chemical::ResidueType const&, bool) const + 265
  
  4 libcore.2.dylib 0x000000010c063711 core::chemical::ResidueTypeSet::generate_residue_type(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 2033
  
  5 libcore.2.dylib 0x000000010c062e9a core::chemical::ResidueTypeSet::name_mapOP(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 74
  
  6 libcore.2.dylib 0x000000010c062d23 core::chemical::ResidueTypeSet::name_map(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 35
  
  7 libcore.2.dylib 0x000000010c056fd2 core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 1794
  
  8 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  9 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  10 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  11 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  12 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  13 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  14 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  15 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  16 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  17 libcore.2.dylib 0x000000010c0572bd core::chemical::ResidueTypeFinder::apply_patches_recursively(utility::vector1<std::__1::shared_ptr<core::chemical::ResidueType const>, std::__1::allocator<std::__1::shared_ptr<core::chemical::ResidueType const> > > const&, unsigned long, bool) const + 2541
  
  18 libcore.2.dylib 0x000000010c058ff8 core::chemical::ResidueTypeFinder::get_all_possible_residue_types(bool) const + 280
  
  19 libcore.2.dylib 0x000000010c06a4b4 core::chemical::ResidueTypeSetCache::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) + 852
  
  20 libcore.2.dylib 0x000000010bfb6bd3 core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(core::chemical::AA, utility::vector1<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, utility::vector1<core::chemical::VariantType, std::__1::allocator<core::chemical::VariantType> > const&) const + 67
  
  21 libcore.4.dylib 0x000000010a0872db core::pack::task::ResidueLevelTask_::ResidueLevelTask_(core::conformation::Residue const&, core::pose::Pose const&) + 859
  
  22 libcore.4.dylib 0x000000010a07f269 core::pack::task::PackerTask_::PackerTask_(core::pose::Pose const&) + 489
  
  23 libcore.4.dylib 0x000000010a0a05e8 core::pack::task::TaskFactory::create_packer_task(core::pose::Pose const&) + 40
  
  24 libprotocols_b.5.dylib 0x0000000105c569ce protocols::abinitio::ResolutionSwitcher::apply(core::pose::Pose&) + 1230
  
  25 libprotocols_b.5.dylib 0x0000000105b903c4 protocols::abinitio::AbrelaxApplication::fold(core::pose::Pose&, std::__1::shared_ptr<protocols::abinitio::Protocol>) + 7748
  
  26 libprotocols_b.5.dylib 0x0000000105b92eef protocols::abinitio::AbrelaxApplication::run() + 351
  
  27 AbinitioRelax.default.macosclangrelease 0x00000001043fd655 main + 501
  
  28 libdyld.dylib 0x00007fff938585ad start + 1
  
  29 ??? 0x0000000000000085 0x0 + 133
  
  Error: Must call shutdown() when finished using job distributor!
  
  protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
  
  Exception :
  
  [ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 349
  
  ERROR: Failed to apply a PatchOperation to CYZ
  
  **********
  
  I would really appreciate any help to solve this.
  
  Thanks,
  
  Subha
- June 8, 2017 at 9:32 pm #12387
  Anonymous
  Is there any reason you should be using CYZ? (It’s not actually in your PDB that way, or anything?) I don’t know where CYZ is coming from if you’ve removed it from the residue type lists (it won’t get loaded in that case). Surely you don’t have it in your FASTA input.
  
  I think -correct is deprecated (although it might not be in the version you are using). If I recall correctly, some of the -correct changes were implemented by a splitting of the database. What do you see in the database near fa_standard? Is one of them likely to be connected to the -correct flag (and if so, try removing CYZ in the same fashion there)?
- June 8, 2017 at 9:32 pm #12908
  Anonymous
  Is there any reason you should be using CYZ? (It’s not actually in your PDB that way, or anything?) I don’t know where CYZ is coming from if you’ve removed it from the residue type lists (it won’t get loaded in that case). Surely you don’t have it in your FASTA input.
  
  I think -correct is deprecated (although it might not be in the version you are using). If I recall correctly, some of the -correct changes were implemented by a splitting of the database. What do you see in the database near fa_standard? Is one of them likely to be connected to the -correct flag (and if so, try removing CYZ in the same fashion there)?
- June 8, 2017 at 9:32 pm #13429
  Anonymous
  Is there any reason you should be using CYZ? (It’s not actually in your PDB that way, or anything?) I don’t know where CYZ is coming from if you’ve removed it from the residue type lists (it won’t get loaded in that case). Surely you don’t have it in your FASTA input.
  
  I think -correct is deprecated (although it might not be in the version you are using). If I recall correctly, some of the -correct changes were implemented by a splitting of the database. What do you see in the database near fa_standard? Is one of them likely to be connected to the -correct flag (and if so, try removing CYZ in the same fashion there)?
- June 9, 2017 at 10:42 pm #12389
  Anonymous
  I did have other fa_standard directories and doing that modification did help. The job is running now, Thanks heaps!. I also see that the -residues:patch_selectors replonly is not available and the program suggested -chemical:patch_selectors replonly (Hope this is a part of some version_control).
  
  Thanks again,
  
  Subha
- June 9, 2017 at 10:42 pm #12910
  Anonymous
  I did have other fa_standard directories and doing that modification did help. The job is running now, Thanks heaps!. I also see that the -residues:patch_selectors replonly is not available and the program suggested -chemical:patch_selectors replonly (Hope this is a part of some version_control).
  
  Thanks again,
  
  Subha
- June 9, 2017 at 10:42 pm #13431
  Anonymous
  I did have other fa_standard directories and doing that modification did help. The job is running now, Thanks heaps!. I also see that the -residues:patch_selectors replonly is not available and the program suggested -chemical:patch_selectors replonly (Hope this is a part of some version_control).
  
  Thanks again,
  
  Subha
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