Hello,
I am using pepspec in design mode, working with a peptide bound to a protein pocket. When I run the command (pepspec.linuxgccrelease -database $ROSETTA_DB @spec.args) I get the following error:
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1.
The spec.args parameters file is:
-in:file:s JM21_final_frame.pdb
-pepspec::pep_chain B
-pepspec::pep_anchor 1
-pepspec::n_peptides 10
-ignore_unrecognized_res
-ex1
-ex2
-extrachi_cutoff 0
-score::weights ref2015.wts
-pepspec::soft_wts soft_rep.wts
-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0
-pepspec::n_build_loop 100
-pepspec::diversify_pep_seqs
-pepspec::diversify_lvl 1
-pepspec::save_low_pdbs
-o test_JM21
.. and the backtrace is:
##############################################################################################################
#
# 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]: 2021.07+release.c48be26
[COMMIT_DATE]: 2021-02-22T05:46:30.047733
[APPLICATION]: pepspec.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "9.3.0"
[STDLIB]: libstdc++ version 20200808
[START_OPTIONS]
-in:ignore_unrecognized_res -in:path:database=/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/database/ -in:file:s=JM21_final_frame.pdb -out:file:o=test_JM21 -score:weights=ref2015.wts -packing:extrachi_cutoff=0 -packing:ex1 -packing:ex2 -pepspec:soft_wts=soft_rep.wts -pepspec:pep_anchor=1 -pepspec:pep_chain=B -pepspec:n_peptides=10 -pepspec:n_build_loop=100 -pepspec:interface_cutoff=5 -pepspec:diversify_pep_seqs -pepspec:diversify_lvl=1 -pepspec:save_low_pdbs -pepspec:clash_cutoff=5
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f8addddce4a]
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x103) [0x7f8adde154e3]
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f8addde1583]
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f8addde119b]
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libprotocols.3.so(core::conformation::Conformation::residue(unsigned long) const+0xf3) [0x7f8ae4093113]
/mnt/d/Softwares/Rosetta/rosetta_src_2021.07.61567_bundle/main/source/build/src/release/linux/5.4/64/x86/gcc/9/default/libcore.3.so(core::pose::Pose::chain(unsigned long) const+0xd) [0x7f8adfdbbf0d]
pepspec.linuxgccrelease(+0x30a1b) [0x555dc8fa4a1b]
pepspec.linuxgccrelease(+0x3963f) [0x555dc8fad63f]
pepspec.linuxgccrelease(+0x1f581) [0x555dc8f93581]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f8add6bb0b3]
pepspec.linuxgccrelease(+0x1f5be) [0x555dc8f935be]
[END_BACKTRACE]
[FILE]: src/core/conformation/Conformation.hh
[LINE]: 509
[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]
I've seen this error is assciated to a previous bug. Any help will be very appreciated.
Best
I solved the problem. I must pack the input pdb previous running pepspec.
Best