[Solved] RosettaAntibody3 – Grafting step is failing to detect H3 from the input sequence

I am trying to run RosettaAntibody3 to build an Fv hhomology model from an input sequence. I am following the documentation form here.

I am using the command: 

antibody.static.linuxgccrelease 

-database $ROSETTA_DATABASE 

-fasta /mnt/data/input/myinput.fasta 

-nstruct 1 

-out:path:all /mnt/data/output/output-graft/ 

-detect_disulf false

 which fails fairly quickly with the error:

protocols.antibody.grafting: Path to REGEX file is: /databases/rosetta/protocol_data/antibody/cdr_regex.txt

protocols.antibody.grafting: The detected H1 REGEX is: C[A-Z]{1,16}(W)(I|V|F|Y|A|M|L|N|G)(R|K|Q|V|N|C|G)(Q|K|H|E|L|R)

protocols.antibody.grafting: The detected H3 REGEX is: C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R)

protocols.antibody.grafting: The detected L1 REGEX is: C[A-Z]{1,17}(WYL|WLQ|WFQ|WYQ|WYH|WVQ|WVR|WWQ|WVK|WYR|WLL|WFL|WVF|WIQ|WYR|WNQ|WHL|WHQ|WYM|WYY)

protocols.antibody.grafting: The detected L3 REGEX is: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)

protocols.antibody.grafting: H1 detected: GFTLEYYAIG (10 residues at positions: 25 to 35)

H3 detection: failed



[ ERROR ]: Caught exception:





File: src/protocols/antibody/grafting/regex_based_cdr_detection.cc:100

H3 detection: failed. Pattern:C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R) 

I know this is a valid sequence – as the antibody itself is a real and functional antibody. 

Does anyone know why RosettaAntibody is failing to detect H3 as is? Is there a way to circumvent this problem?

As a hack, I changed the cdr_regex.txt to replace the H3 line with `H3 “<MyKnownH3Sequence>”`, and it still failed.