I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb.
However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).
Is there any way to runn RAbD while FIXing all the CDRs?
My command is:
$ROSETTA_BIN/antibody_designer.macosclangrelease \ -database $ROSETTA_DATABASE \ -do_dock \ -use_epitope_constraints \ -in:file:s complex_start.pdb \ -cdr_instructions instr.txt
My instr.txt file is:
# No design ALL GraftDesign FIX ALL SeqDesign FIX ALL MinProtocol MINTYPE relax
And the error I am seeing is:
ERROR: No CDRs to design! Please set CDRs via instructions file, cmd-line, or RosettaScripts!
Is there any way to have RAbD run without implementing the grafting and sequence design steps?