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

[Anonymous]

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!

 

[Anonymous]

I should also mention that I am using Rosetta 3.12.

[Anonymous]

“No input sequences” seems self explanatory. In the instructions you linked there is talk of a  “-fasta” attribute in the second paragraph. Maybe it’s that that is missing?

[Anonymous]

Looks like you are correct. The flags

-fasta myfasta.fa -vhh_only

are indeed requred for the antibody_H3 application. This was pretty unclear in the documentation, so thank you for bringing it up.

NOTE: obviously, the vhh_only flag is only required whenn modeling single heavy chain antibodies.

[Anonymous]

  

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