“core.kinematics.FoldTree” error upon running RAbD

[Anonymous]

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!

[Anonymous]

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.  

[Anonymous]

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!

[Author]

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