'std::out_of_range' Error in Relax with noncanonical amino acids

[zrpeak]

I am investigating the effect of mutations with noncanonical amino acids (NCAAs) on protein-protein interface. I have generated the params file for my NCAA with mol_to_params.py and the Relax of the NCAA incorporated protein complex goes well initially. However, when I tried to change the position that NCAA incorporates, or delete one of the protein in the complex, the Relax program crashed with the error below:

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.


terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at
Got some signal... It is:6
Signal 6 (SIGABRT) means that the process was aborted.  This usually means an internal Rosetta error caused by (often) bad inputs, (sometimes) developer error, or (rarely) hardware problems.

And below is the crash log:

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2023.45+release.a6d9ba8
[COMMIT_DATE]: 2023-11-07T23:58:11.511241
[APPLICATION]: /home/peak/Downloads/rosetta.source.release-362/main/source/bin/relax.mpi.linuxgccrelease
[MODE]: Release
[EXTRAS]: mpi (OpenMPI 4.1.4) 
[OS]: GNU/Linux
[COMPILER]: GCC version "13.2.1 20231011 (Red Hat 13.2.1-4)"
[STDLIB]: libstdc++ version 20231011
[START_OPTIONS]
 -in:file:s=Y56ONBY.pdb -in:file:extra_res_fa=NBY.params -out:nstruct=40 -packing:no_optH=false -packing:flip_HNQ -packing:ex1 -packing:ex2 -relax:constrain_relax_to_start_coords -relax:ramp_constraints=false

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7fdafe1a3553]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libutility.so(+0x18b89f) [0x7fdafe18b89f]
/lib64/libstdc++.so.6(+0xb4f4c) [0x7fdafcab4f4c]
/lib64/libstdc++.so.6(+0xb4fb7) [0x7fdafcab4fb7]
/lib64/libstdc++.so.6(+0xb5218) [0x7fdafcab5218]
/lib64/libstdc++.so.6(std::__throw_out_of_range(char const*)+0x40) [0x7fdafcaa7738]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.7.so(core::chemical::ResidueType::atom_index(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const+0x1c2) [0x7fdb0b968742]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libcore.3.so(core::pose::addVirtualResAsRoot(numeric::xyzVector<double> const&, core::pose::Pose&)+0x631) [0x7fdb0050b3f1]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libcore.3.so(core::pose::addVirtualResAsRoot(core::pose::Pose&)+0x2b) [0x7fdb0050b80b]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.4.so(protocols::relax::RelaxProtocolBase::set_up_constraints(core::pose::Pose&, core::kinematics::MoveMap&)+0x899) [0x7fdb069f2449]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.4.so(protocols::relax::FastRelax::apply(core::pose::Pose&)+0x564) [0x7fdb069c6834]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0x20b8) [0x7fdb03ecf478]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x214) [0x7fdb03ecfff4]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x46) [0x7fdb03eb5946]
/home/peak/Downloads/rosetta.source.release-362/main/source/build/src/release/linux/6.5/64/x86/gcc/13/mpi/libprotocols.4.so(protocols::relax::Relax_main(bool)+0xa0c) [0x7fdb069e91fc]
/home/peak/Downloads/rosetta.source.release-362/main/source/bin/relax.mpi.linuxgccrelease() [0x40119e]
/lib64/libc.so.6(+0x27b8a) [0x7fdafc849b8a]
/lib64/libc.so.6(__libc_start_main+0x8b) [0x7fdafc849c4b]
/home/peak/Downloads/rosetta.source.release-362/main/source/bin/relax.mpi.linuxgccrelease() [0x4011d5]

[END_BACKTRACE]

[FILE]: St12out_of_range
[LINE]: 0
[START_MESSAGE]
map::at

[END_MESSAGE]
[END_CRASH_REPORT]

The NCAA params file seemed to be OK, as the Relax program worked well in several different positions. Any help is greatly appreciated and I am happy to supply any other information/files that may be helpful in debugging.