Antibody Modelling

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    • January 24, 2017 at 5:30 am #2578
      Anonymous

        Hi,

        I’m trying to run antibody.linuxgccrelease -fasta antibody.fasta|tee grafting.log but got this error

        terminate called after throwing an instance of ‘std::out_of_range’

          what():  basic_string::substr: __pos (which is 3) > this->size() (which is 0)

        protocols.antibody.grafting: Setting antibody grafting database path from command line-options to: /import/kamen/3/z5038596/ToR/rosetta/tools/antibody

        protocols.antibody.grafting: Setting output prefix from command line-options to: grafting/

        protocols.antibody.grafting: Setting path to NCBI-Blast+ executable from command line-options to: blastp

        basic.execute: Running blast+ for frh… blastp -db /ToR/rosetta/tools/antibody/blast_database/database.FRH -query grafting/frh.fasta -out grafting/frh.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 0.00001 -matrix BLOSUM62

        The blastp is up to date and its path is correct.

      • January 24, 2017 at 3:16 pm #12115
        Anonymous

          I hadn’t run into tee before, cool utility!

          Best guess off the top of my head is that RosettaAntibody doesn’t like your input sequence – it thinks one of the CDR loops is too long or short or something.

          We may get more information if you try with “-out:level 500”, or try compiling and running in debug mode.

        • January 24, 2017 at 3:16 pm #12636
          Anonymous

            I hadn’t run into tee before, cool utility!

            Best guess off the top of my head is that RosettaAntibody doesn’t like your input sequence – it thinks one of the CDR loops is too long or short or something.

            We may get more information if you try with “-out:level 500”, or try compiling and running in debug mode.

          • January 24, 2017 at 3:16 pm #13157
            Anonymous

              I hadn’t run into tee before, cool utility!

              Best guess off the top of my head is that RosettaAntibody doesn’t like your input sequence – it thinks one of the CDR loops is too long or short or something.

              We may get more information if you try with “-out:level 500”, or try compiling and running in debug mode.

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