I am tryig to use RosettaAntibody3 to build a homology model for my antibody sequence. I am following the protocol workflow outlined in detail here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol. The only difference is that I am modleing a VHH (heavy chain only antibody).
I am run the grafting tool without issue with results in an output model (grafting/model-0.pdb), exactly as the protocol states it should. I then fed that PDB into the antibody_h3 application, and am hit with the error:
[ ERROR ]: Caught exception: File: src/apps/public/antibody/antibody.cc:205 [ ERROR ] UtilityExitException ERROR: Error: no input sequences were specified!
I have no idea what this means, or how to address it since I am trying to follow the protocol almost exactly.
The full command I am running is:
antibody_H3.linuxgccrelease \ -database $ROSETTA_DATABASE \ -s grafting/model-0.pdb \ -antibody:auto_generate_kink_constraint true \ -antibody:constrain_vlvh_qq true \ -constraints:cst_weight 1.0 \ -ex1 \ -ex2 \ -extrachi_cutoff 0 \ -out:file:scorefile /output/myantibody.score \ -antibody:all_atom_mode_kink_constraint \ -out:path:all /output/ \ -nstruct 1 \ // Set to 1 for testing -overwrite
Does anyone have any idea what this error means in the context of using RosettaAntibody3 to build a homology model, specifically a VHH?