Dear all,
I am trying to running RAbD with the following command:
antibody_designer.linuxgccrelease \
-l design_input.list \
-primary_cdrs H3 \
-graft_design_cdrs H3 \
-seq_design_cdrs H1 H2 \
-do_dock \
-paratope H3 \
-mc_optimize_dG \
-mc_total_weight .001 \
-mc_interface_weight .999 \
-out:path:all designing\
-out:file:scorefile designing_scores.fasc\
-nstruct 3 | tee designing.log
Strangely, the command sucessfully produce the some designed structures but I get the following error output information:
core.kinematics.FoldTree: (1) [ FATAL ] FoldTree::edge_label(...) edge not in tree: 68 289
What could be the possible reason and is it possible to correct it?
Best regards!
Category:
Post Situation:
Does your input structure have anything different with it? Any glycans, ligands, or post-translational modifications? Sometimes it's that. If RAbD produced results, I wouldn't worry about it too much. But if you have the full log, that would be helpful for me to debug it. It may just be Rosetta chatter, or a particular H3 that didn't graft well.
The input structures have no glycans, ligands, or post-translational modifications. They are just models of ag-ab complexes built with Rosetta antibody and H3-modeling from the primary sequences and the Rosetta docking.protocol. It is possible that a particular H3 that didn't graft well. But I hope that RAbD won't stop just because there is a problem with only one input structure in the input list. The full log file can be found at:
https://drive.google.com/file/d/18d6xmpJMD5NGHIlWnKS7muPnRztilwyB/view?usp=sharing
Thanks!