'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.

[roccomoretti]

It looks like the error you're getting is due to an assumption that a PROTEIN residue has a CA atom. (That is, an atom named "CA".) If that's not the case, you'll see the error you do here.

You're seeing the issue because the constrain-to-start mechanism adds a virtual root atom, and the faulty assumption is in the virtual root addition code.

There really isn't a good workaround, aside from A) not using the constraint-to-start code, B) renaming the atoms in your NCAA to include a CA atom or C) make sure that your non-CA-containing NCAA isn't in the middle third of the protein. (For some reason the virtual root code only works with the middle third of the system.)

[zrpeak]

I have modified the ATOM names in both the params file and the input PDB file, and the Relax program can finish without crash now. Thank you very much!