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

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RosettaAntibody3 is failing with "Error: no input sequences were specified!"
#1

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!

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Sun, 2020-08-16 16:16
brspurri

I should also mention that I am using Rosetta 3.12.

Sun, 2020-08-16 18:51
brspurri

"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
matteoferla

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
brspurri
Tue, 2020-08-18 09:57
brspurri