Hello,
I successfully ran snugdock protocol and generated 1000 poses. But I need interface rmsd of these docked poses *against the native complex* for further analysis. While re-running snugdock with the native complex, I'm getting the "ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues." error. I have checked the no. of residues, numbering and order and can't figure out what I'm doing wrong. I have attached my input files (input file was >512 KB so I divided it into input1.pdb and input2.pdb), rosetta_crash.log and native complex pdb.
I'm using the following flags:
mpirun -np 20 $ros/bin/snugdock.mpi.linuxgccrelease \
-s $pdb \
-native $pdb_native \
-out:file:scorefile score_out_snugdock.sc \
-out:path:pdb models_output/ \
-out:pdb_gz \
-spin \
-dock_pert 3 8 \
-ex1 \
-ex2aro \
-nstruct 2 \
-partners LH_VW \
-ensemble1 antibody.list.ensemble \
-ensemble2 antigen.list.ensemble \
-h3_filter false \
-kic_rama2b \
-loops:ramp_fa_rep \
-loops:ramp_rama \
-kic_omega_sampling \
-allow_omega_move true \
-loops:refine_outer_cycles 1 \
-loops:max_inner_cycles 1 \
-rebuild_disulf false \
-detect_disulf false \
-ignore_unrecognized_res \
This is how my ROSETTA_CRASH.log looks like:
##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.36+release.57ac713
[COMMIT_DATE]: 2021-09-12T14:52:42.922397
[APPLICATION]: /home/apps/centos7/Rosetta/2021.38/main/source/bin/snugdock.mpi.linuxgccrelease
[MODE]: Release
[EXTRAS]: mpi (OpenMPI 4.0.2)
[OS]: GNU/Linux
[COMPILER]: GCC version "6.5.0"
[STDLIB]: libstdc++ version 20181026
[START_OPTIONS]
-in:ignore_unrecognized_res -in:detect_disulf=false -in:file:s=input.pdb -in:file:native=native.pdb -out:overwrite -out:nstruct=2 -out:pdb_gz -out:mpi_tracer_to_file=tracer1.log -out:file:scorefile=score_out_snugdock.sc -out:path:pdb=models_output/ -run:rebuild_disulf=false -packing:ex1 -packing:ex2aro -loops:allow_omega_move -loops:refine_outer_cycles=1 -loops:max_inner_cycles=1 -loops:kic_omega_sampling -loops:ramp_fa_rep -loops:ramp_rama -loops:kic_rama2b -antibody:h3_filter=false -docking:partners=LH_VW -docking:spin -docking:dock_pert=3 8 -docking:ensemble1=antibody.list.ensemble -docking:ensemble2=antigen.list.ensemble
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libutility.so(backtrace_string[abi:cxx11](int)+0x42) [0x2af84293cb32]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe2) [0x2af84289c9d2]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xfc) [0x2af84294242c]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x36) [0x2af8429421f6]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols.7.so(core::conformation::Conformation::residue(unsigned long) const+0x92) [0x2af8323bbc02]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols_h.5.so(protocols::docking::calc_Lrmsd(core::pose::Pose const&, core::pose::Pose const&, utility::vector1<int, std::allocator<int> >)+0x302) [0x2af8360e70e2]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols_h.5.so(protocols::docking::DockingProtocol::apply(core::pose::Pose&)+0xb00) [0x2af8360a16c0]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols.7.so(protocols::antibody::snugdock::SnugDockProtocol::apply(core::pose::Pose&)+0x301) [0x2af832aa03e1]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/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)+0xfa0) [0x2af83c430bf0]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x156) [0x2af83c432dc6]
/home/apps/centos7/Rosetta/2021.38/main/source/build/src/release/linux/3.10/64/x86/gcc/6.5/mpi/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x47) [0x2af83c419397]
/home/apps/centos7/Rosetta/2021.38/main/source/bin/snugdock.mpi.linuxgccrelease() [0x408c3f]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2af845e28555]
/home/apps/centos7/Rosetta/2021.38/main/source/bin/snugdock.mpi.linuxgccrelease() [0x408d3f]
[END_BACKTRACE]
[FILE]: src/core/conformation/Conformation.hh
[LINE]: 514
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose.
[END_MESSAGE]
[END_CRASH_REPORT]
The program runs fine if I remove the 'native' flag but I need interface rmsd values.
I also ran score_jd2 protocol but it doesn't seem to give irmsd values either. Is there any other way to get irmsd values?
Thank you.
