Hello all, I am using the antibody.mpi.linuxgccrelease to model multiple antibodies. Most work fine but about 10% are failing with weird error messages. I have tried everything to figure out the problem but am having no luck. These antibodies are clinical molecules, and so I feel like my failure rate is pretty high, and I'm probably doing something wrong. There is not a lot of documentation about the (newer) antibody homology modelling application and so I am a little bit at a loss as what to do to make the program more robust. Thanks as usual for all your help!!!
For example 1
ocrelizumab
>heavy
EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYNMHWVRQAPGKGLEWVGAIYPGNGDTSYNQKFKGRFTISVDKSKNTLYLQMNSLRAEDTAVYYCARVVYYSNSYWYFDVWGQGTLVTVSS
>light
DIQMTQSPSSLSASVGDRVTITCRASSSVSYMHWYQQKPGKAPKPLIYAPSNLASGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQWSFNPPTFGQGTKVEIK
errors with:
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1.
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 507
ROSETTA_CRASH.log
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x36) [0x7f3f231cbb96]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols.7.so(core::conformation::Conformation::residue(unsigned long) const+0xda) [0x7f3f2f68a3da]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols.7.so(protocols::antibody::grafting::construct_antibody(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x275f) [0x7f3f2f0b52ef]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols.7.so(protocols::antibody::grafting::graft_cdr_loops(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)+0xc6) [0x7f3f2f0b8da6]
antibody.mpi.linuxgccrelease() [0x41aa54]
antibody.mpi.linuxgccrelease() [0x41716a]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f3f21b8a3d5]
antibody.mpi.linuxgccrelease() [0x4172c5]
[END_BACKTRACE]
[FILE]: src/core/conformation/Conformation.hh
[LINE]: 507
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1.
[END_MESSAGE]
[END_CRASH_REPORT]
Radretumumab Example 2
radretumab
>heavy
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSFSMSWVRQAPGKGLEWVSSISGSSGTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKPFPYFDYWGQGTLVTVSS
>light
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSFLAWYQQKPGQAPRLLIYYASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQTGRIPPTFGQGTKVEIK
errors with:
core.conformation.util: (0) [ ERROR ] Residue 1 was disulfide bonded but had no partner
ERROR:: Exit from: src/core/conformation/util.cc line: 2402
[ ERROR ]: Caught exception:
File: src/core/conformation/util.cc:2402
[ ERROR ] UtilityExitException
ERROR:
ROSETTA_CRASH.log
[COMPILER]: GCC version "7.5.0"
[STDLIB]: libstdc++ version 20191114
[START_OPTIONS]
-fasta=radretumab.fas
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libcore.6.so(backtrace_string[abi:cxx11](int)+0x43) [0x7f28251d4f13]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xd3) [0x7f28207c4c33]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xfb) [0x7f2820786f3b]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x36) [0x7f2820786b96]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols_b.6.so(utility::exit(char const*, int, int)+0x29) [0x7f282af520b9]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libcore.2.so(core::conformation::disulfide_bonds(core::conformation::Conformation const&, utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >&)+0x296) [0x7f28217f9ab6]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols_a.5.so(protocols::grafting::insert_pose_into_pose(core::pose::Pose const&, core::pose::Pose const&, unsigned long, unsigned long, bool)+0x9b) [0x7f28289b06eb]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols_a.5.so(protocols::grafting::GraftMoverBase::insert_piece(core::pose::Pose const&, core::pose::Pose&)+0xb7) [0x7f28289ab9c7]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols_a.5.so(protocols::grafting::CCDEndsGraftMover::apply(core::pose::Pose&)+0x18e) [0x7f28289a720e]
/SFS/user/ry/waight/tools/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.5/mpi/libprotocols.7.so(protocols::antibody::grafting::graft_cdr_loops(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)+0xe67) [0x7f282c673b47]
antibody.mpi.linuxgccrelease() [0x41aa54]
antibody.mpi.linuxgccrelease() [0x41716a]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f281f1453d5]
antibody.mpi.linuxgccrelease() [0x4172c5]
[END_BACKTRACE]
[FILE]: src/core/conformation/util.cc
[LINE]: 2402
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR:
[END_MESSAGE]
[END_CRASH_REPORT]
Olaratumab Example 3
>heavy
QLQLQESGPGLVKPSETLSLTCTVSGGSINSSSYYWGWLRQSPGKGLEWIGSFFYTGSTYYNPSLRSRLTISVDTSKNQFSLMLSSVTAADTAVYYCARQSTYYYGSGNYYGWFDRWDQGTLVTVSS
>light
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPAFGQGTKVEIK
Im just getting a failure to find the CDR H3
protocols.antibody.grafting: (0) H1 detected: GGSINSSSYYWG (12 residues at positions: 25 to 37)
H3 detection: failed
[ ERROR ]: Caught exception:
File: src/protocols/antibody/grafting/regex_based_cdr_detection.cc:100
H3 detection: failed. Pattern:C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R) query:QLQLQESGPGLVKPSETLSLTCTVSGGSINSSSYYWGWLRQSPGKGLEWIGSFFYTGSTYYNPSLRSRLTISVDTSKNQFSLMLSSVTAADTAVYYCARQSTYYYGSGNYYGWFDRWDQGTLVTVSS