I'm trying to run abinitio to predict the structure of a mutant protein homologue. using thwe following command line options:
AbinitioRelax.macosclangrelease -in:file:native ./input_files/input.pdb -in:file:fasta ./input_files/ACSM3.txt -in:file:frag3 ./input_files/aat000_03_05.200_v1_3 -in:file:frag9 ./input_files/aat000_09_05.200_v1_3 -database $ROSETTA3_DB -nstruct 1 -out:path ./output_files/ -out:pdb -abinitio::increase_cycles 10 -abinitio:rg_reweight 0.5 -abinitio:rsd_wt_helix 0.5 -abinitio:rsd_wt_loop 0.5
When I run this programme I end up with the following last lines before termination ...
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader...
libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
Abort trap: 6
I'm running Rosetta 3.8 and I'd appreciate any help.
I've managed to solve this error by checking the fragment files. Turns out they were missing parts of it so I re copied and programme is running fine.