antibody.mpi.linuxgccrelease some antibodies failing to model

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