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

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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: 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/
[ 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


Does anyone have any idea what this error means in the context of using RosettaAntibody3 to build a homology model, specifically a VHH?



Post Situation: 
Sun, 2020-08-16 16:16

I should also mention that I am using Rosetta 3.12.

Sun, 2020-08-16 18:51

"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?

Mon, 2020-08-17 05:04

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.

Tue, 2020-08-18 09:32


Tue, 2020-08-18 09:57