Hello,
I want to generate a macrocycle of a 10 residues peptide, that has an amidated C-terminal residue.
For this, I am playing with simple_cycpep_predict with the -cyclic_peptide:cyclization_type sidechain_isopeptide flag to get crosslinked sidechains between positions 5 and 10, i.e, LYS5 ... ASP10 (ASP10 is amidated). I have a lineal peptide pdb of the same sequence that I would use as native). My command line and flags are:
mpirun -n 8 simple_cycpep_predict.mpi.linuxgccrelease -database $ROSETTA_DB \
-cyclic_peptide:sequence_file $sequence \
-in:file:native $native \
-cyclic_peptide:cyclization_type sidechain_isopeptide \
-cyclic_peptide:sidechain_isopeptide_indices 5 10 \
-cyclic_peptide:disulf_cutoff_prerelax 100 \
-cyclic_peptide:disulf_cutoff_postrelax 1 \
-cyclic_peptide:genkic_closure_attempts 1000 \
-cyclic_peptide:genkic_min_solution_count 100 \
-cyclic_peptide:min_genkic_hbonds 0 \
-cyclic_peptide:MPI_auto_2level_distribution \
-cyclic_peptide:MPI_batchsize_by_level 10 \
-cyclic_peptide:MPI_sort_by energy \
-score:symmetric_gly_tables true \
-extra_patch_fa $PATCH_PATH/Cterm_amidation.txt \
-mute all -unmute protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary \
-out:nstruct 1000 \
-out:file:silent output_$filename.silent
... but I get the following error:
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2022.11+release.512e589
[COMMIT_DATE]: 2022-03-14T17:54:23.772418
[APPLICATION]: simple_cycpep_predict.mpi.linuxgccrelease
[MODE]: Release
[EXTRAS]: mpi (OpenMPI 1.10.2)
[OS]: GNU/Linux
[COMPILER]: GCC version "5.4.0 20160609"
[STDLIB]: libstdc++ version 20160609
[START_OPTIONS]
-in:path:database=/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/database/ -in:file:native=10mers_Ct_amidated_0001_relax.pdb -in:file:extra_patch_fa=/mnt/data/yalmeida/Softwares/Rosetta/3.13/rosetta_src_2021.16.61629_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/Cterm_amidation.txt -out:nstruct=1000 -out:mute=all -out:unmute=protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary -out:file:silent=output_JM21_10mers_NH2.silent -score:symmetric_gly_tables -cyclic_peptide:cyclization_type=sidechain_isopeptide -cyclic_peptide:sequence_file=JM21_10mers_NH2.res -cyclic_peptide:genkic_closure_attempts=1000 -cyclic_peptide:genkic_min_solution_count=100 -cyclic_peptide:min_genkic_hbonds=0 -cyclic_peptide:disulf_cutoff_prerelax=100 -cyclic_peptide:disulf_cutoff_postrelax=1 -cyclic_peptide:sidechain_isopeptide_indices=5 10 -cyclic_peptide:MPI_auto_2level_distribution -cyclic_peptide:MPI_batchsize_by_level=10 -cyclic_peptide:MPI_sort_by=energy
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x33) [0x14e4d0cf7c33]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libutility.so(utility::terminate_handler()+0x184) [0x14e4d0cf8084]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d6b6) [0x14e4d05746b6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d701) [0x14e4d0574701]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d919) [0x14e4d0574919]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::__throw_out_of_range(char const*)+0x3f) [0x14e4d059d2cf]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(core::pose::Pose&, core::pose::Pose const&, bool) const+0xba4) [0x14e4d5556a14]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run() const+0x17a1) [0x14e4d5570d91]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI::derived_worker_carry_out_n_jobs(unsigned long, utility::vector1<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary>, std::allocator<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary> > >&, utility::vector1<std::shared_ptr<core::io::silent::SilentStruct>, std::allocator<std::shared_ptr<core::io::silent::SilentStruct> > >&, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::pose::Pose const>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const+0x24c) [0x14e4d557f25c]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::HierarchicalHybridJDApplication::worker_carry_out_njobs(unsigned long&, utility::vector1<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary>, std::allocator<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary> > >&, utility::vector1<std::shared_ptr<core::io::silent::SilentStruct>, std::allocator<std::shared_ptr<core::io::silent::SilentStruct> > >&) const+0xbb) [0x14e4d5519a3b]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::HierarchicalHybridJDApplication::run_worker() const+0xbe) [0x14e4d552ab2e]
simple_cycpep_predict.mpi.linuxgccrelease() [0x40310b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x14e4cff27840]
simple_cycpep_predict.mpi.linuxgccrelease() [0x4038c9]
[END_BACKTRACE]
[FILE]: St12out_of_range
[LINE]: 0
[START_MESSAGE]
map::at
[END_MESSAGE]
[END_CRASH_REPORT]
Any idea what is going wrong?
Thanks in advance
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