core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

Dear developers,  

I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

This is my command line: 

antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta

and this is the content of  ROSETTA_CRASH.log:

##############################################################################################################

#

# 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]: 2020.08+release.cb1caba

[COMMIT_DATE]: 2020-02-22T18:49:33.865989

[APPLICATION]: antibody.default.linuxgccrelease

[MODE]: Release

[EXTRAS]: default

[OS]: GNU/Linux

[COMPILER]: GCC version "7.3.0"

[STDLIB]: libstdc++ version 20180125

[START_OPTIONS]

 -in:ignore_unrecognized_res -fasta=antibody_chains.fasta

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7fd0dfe544b3]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libutility.so(utility::signal_handler(int)+0xd4) [0x7fd0dfe545d4]

/lib64/libc.so.6(+0x36400) [0x7fd0ddda7400]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libcore.2.so(core::conformation::Residue::Residue(core::chemical::ResidueType const&, core::conformation::Residue const&, core::conformation::Conformation const&, bool, bool)+0x24) [0x7fd0e1673424]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libcore.2.so(core::conformation::ResidueFactory::create_residue(core::chemical::ResidueType const&, core::conformation::Residue const&, core::conformation::Conformation const&, bool, bool)+0x79) [0x7fd0e1678259]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libprotocols.3.so(protocols::simple_moves::MutateResidue::make_mutation(core::pose::Pose&, unsigned long)+0xb5) [0x7fd0e80141f5]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libprotocols.3.so(protocols::simple_moves::MutateResidue::apply(core::pose::Pose&)+0x2b8) [0x7fd0e8017bb8]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libprotocols.7.so(protocols::antibody::grafting::construct_antibody(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x1dbc) [0x7fd0ef0aa99c]

/mnt/lustre/users/k1513213/rosetta/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/7.3/default/libprotocols.7.so(protocols::antibody::grafting::graft_cdr_loops(protocols::antibody::grafting::AntibodySequence const&, protocols::antibody::grafting::SCS_ResultSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)+0xc6) [0x7fd0ef0aed76]

antibody.default.linuxgccrelease() [0x41ae74]

antibody.default.linuxgccrelease() [0x41740a]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0ddd93555]

antibody.default.linuxgccrelease() [0x417565]

[END_BACKTRACE]

[FILE]: SIGSEGV

[LINE]: 11

[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]

[END_CRASH_REPORT]

I saw that other users had the problem and you suggested to add the -ignore_unrecognized_res flag to command to start the protocol which I did but with not results. It looks like the -gnore_unrecognized_res option had no effect . Also, I noticed that other users had the same problem and the option did not work for them either.

Can you please help me with this? I have attached the antibody_chains.fasta  file too.

Best wishes

Alfredo