I am trying to design a nanobody using an available antibody. After grafting heavy chains from an antibody to a known nanobody scaffold, and aligning with the antibody-antigen complex structure, I obtain nanobody-antigen compelx structure. I am trying to use Rosetta design to increase its affinity to antigen as well as sample possible new CDR sequences using the options,
-graft_design_cdrs H1 H2 H3 -seq_design_cdrs H1 H2 H3 -nstruct 10000 -out:prefix graft -mc_optimize_dG -mc_total_weight .001 -mc_interface_weight .999 -do_dock -use_epitope_constraints -mintype relax -seq_design_profile_samples 5
However out of 10,000 outputs half of them contain original input sequence, with all of them having the same total score, dG seprated and all the other score parameters. Additionally, for rest of the designs the total score is high (in positive 1000s). During the run, I often keep getting the error message like this:
[FILE]: src/core/kinematics/FoldTree.cc [LINE]: 1105 [START_MESSAGE] [ ERROR ] UtilityExitException ERROR:
While the task continues to run. Is there a way to increase the sequence variability or to filter out the orginal sequences from the output?
-Thanks in advance!