RosettaAntibody3 is failing with “Error: no input sequences were specified!”

Hi all,

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?

Thanks!