Error reading in/out glycosylated silent file – “Can’t create a polymer bond after residue due to incompatible type”

[Anonymous]

Hi all,

I’m having trouble extracting (or reading in) a previously rosetta glycoslylated structure from a silent file after relaxing it. Attempting to either extract or read back in the relaxed structure from a silent file results in the following error:

 

Can’t create a polymer bond after residue 506 due to incompatible type: ->4)-alpha-D-Glcp:non-reducing_end

 

The protocol I used is as followes:

I first used the SimpleGlycosylateMover to add a number of sugars to a protein. 

/main/source/bin/rosetta_scripts.mpi.linuxgccrelease -parser:protocol glycosolate.xml -use_input_sc -ex1 -ex2 -ex1aro -ex2aro -s protein_0068.pdb -nstruct 10 -include_sugars -auto_detect_glycan_connections -maintain_links -write_pdb_link_records

This output regular pdb fies with the desires sugars, no problem. 

I then relaxed those regular pdbs using a combinatin of FastRelax and GlycanSampler, output to a silent file.

/main/source/bin/rosetta_scripts.mpi.linuxgccrelease -parser:protocol glyco_relax.xml -use_input_sc -ex1:level 4 -ex2:level 4 -ex1aro:level 6 -ex2aro:level 6 -out:file:silent all_glyco.out -l lst.lst -nstruct 10 -no_his_his_pairE -packing:linmem_ig 25 -include_sugars -auto_detect_glycan_connections -maintain_links -write_pdb_link_records

This completed successfully with no errors and output a silent file. 

 

The problem I encounter is when I try to either extract from the resulting silent file (extract_pdbs) or read back in from the silent file (score_jd2) using, what I think, are appropriate flags.

/main/source/bin/extract_pdbs.mpi.linuxgccrelease -in:file:silent ../all_glyco.out -mute all -ignore_unrecognized_res -include_sugars -alternate_3_letter_codes pdb_sugar -auto_detect_glycan_connections -maintain_links -write_pdb_link_records -load_PDB_components false

or

/main/source/bin/score_jd2.mpi.linuxgccrelease -in:file:silent ../all_glyco.out -in::file::tags protein_Glcp_0005 -ignore_unrecognized_res -include_sugars -alternate_3_letter_codes pdb_sugar -auto_detect_glycan_connections -maintain_links -write_pdb_link_records -load_PDB_components false

EIther of these above methods of reading in/out the glycosylated structures from the silent file results in the following error (I included as many flags as I could find that might be relevant. I’m sure most of the do nothing, but even if I remove them I get the same error below):

 

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.08+release.cb1caba

[COMMIT_DATE]: 2020-02-22T18:49:33.865989

[APPLICATION]: /home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_pdbs.mpi.linuxgccrelease

[MODE]: Release

[EXTRAS]: mpi (OpenMPI 2.1.1) 

[OS]: GNU/Linux

[COMPILER]: GCC version “7.5.0”

[STDLIB]: libstdc++ version 20191114

[START_OPTIONS]

 -in:ignore_unrecognized_res -in:include_sugars -in:auto_detect_glycan_connections -in:alternate_3_letter_codes=pdb_sugar -in:maintain_links -in:file:load_PDB_components=false -in:file:silent=../all_glyco.out -out:mute=all -out:file:write_pdb_link_records

 

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.6.so(backtrace_string[abi:cxx11](int)+0x56) [0x7f87775391d6]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe3) [0x7f8773a990e3]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.2.so(core::conformation::Conformation::append_residue_by_bond(core::conformation::Residue const&, bool, int, unsigned long, int, bool, bool)+0x78e) [0x7f87749ccf0e]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.3.so(core::pose::make_pose_from_sequence(core::pose::Pose&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > >, bool)+0x77d) [0x7f877591b00d]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.3.so(core::pose::make_pose_from_sequence(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool, bool)+0x229) [0x7f87759262f9]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.3.so(core::io::silent::BinarySilentStruct::fill_pose(core::pose::Pose&, core::chemical::ResidueTypeSet const&, bool) const+0xe2) [0x7f8776735362]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.3.so(core::io::silent::BinarySilentStruct::fill_pose(core::pose::Pose&, bool) const+0x77) [0x7f8776732107]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/7/mpi/libcore.6.so(core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(core::pose::Pose&, bool)+0x3a5) [0x7f87774217b5]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_pdbs.mpi.linuxgccrelease(+0x98f4) [0x56446c34b8f4]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f8772c66bf7]

/home/ubuntu/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_pdbs.mpi.linuxgccrelease(+0xa21a) [0x56446c34c21a]

 

[END_BACKTRACE]

 

[FILE]: src/core/conformation/Conformation.cc

[LINE]: 1061

[START_MESSAGE]

Can’t create a polymer bond after residue 506 due to incompatible type: ->4)-alpha-D-Glcp:non-reducing_end

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

 

Any ideas or suggestions for how to solve this issue woudl be appreciated.

Many thanks in advance.

 

-Andrew

 

 

 

 

 

 

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