Hi there,
I tried to do antibody modeling, however, there is complie issue shown as the following:
$ROSETTA/bin/antibody.linuxgccrelease -fasta 27666.fasta | tee grafting.log
ERROR: ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody grafting.
ERROR:: Exit from: src/protocols/antibody/grafting/regex_based_cdr_detection.cc line: 47
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712
core.init: command: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/antibody.linuxgccrelease -fasta 27666.fasta
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2018409100 seed_offset=0 real_seed=-2018409100
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2018409100 RG_type=mt19937
core.init: Resolved executable path: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/antibody.default.linuxgccrelease
core.init: Looking for database based on location of executable: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/database/
antibody: Using antibody grafting_database at: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/database/additional_protocol_data/antibody/
antibody: Unzipping files in antibody_database (if any). This will only be done once.
antibody: Done unzipping.
antibody: Heavy chain fasta input file: 27666.fasta
antibody: Light chain fasta input file: 27666.fasta
antibody: Antibody grafting protocol Running with input:
antibody: SCS_MultiTemplate protocol enabled multi-template regions: orientation
antibody: Heavy chain sequence:
antibody: Light chain sequence:
[ ERROR ]: Caught exception:
File: src/protocols/antibody/grafting/regex_based_cdr_detection.cc:47
[ ERROR ] UtilityExitException
ERROR: ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody grafting.
May I know how to solve this problem?
Thanks,
Yu
The issue is that the copy of Rosetta that you're using was compiled with a slightly older compiler, one which does not fully support all the features which Rosetta uses. Unfortunately, the compiler used to make the pre-compiled Linux binaries which the RosettaCommons provides is one of these compilers.
What you'll need to do is to (re-)compile Rosetta using a "newer" compiler. This would be GCC 5.2 or later or Clang 3.4 or later. See https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation for more information on how to build Rosetta yourself. See the Troubleshooting section for more info on how to specify a particular compiler. (Provide the full path to the updated compilers if you're installing it alongside the existing system compiler.)