Hi All,
I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:
ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol:
File: src/core/kinematics/FoldTree.cc:2317
[ ERROR ] UtilityExitException
ERROR: FoldTree:: residue_edge is undefined for root vertex
I thought that this might be due to the membrane residue, as in the instructions it states that ''Ligands must be last residues in the pdb". In my case, the ligands are two hemes, however, when the membrane residue is built, this then becomes the last residue.
Is there any simple fix for this? Or is it a problem with Coupled Moves and RosettaMP? I haven't found any documentation about the compatibility of RosettaMP and franklin2019 with coupled moves.
Thanks
Ben
"I haven't found any documentation about the compatibility of RosettaMP and franklin2019 with coupled moves. "
I doubt there is any: you are the first person I am aware of to try to use franklin19 with coupled moves. I think your diagnosis is correct. No simple solutions come to mind.
CM needs the ligands last more for iteration purposes than FoldTree purposes if I recall, so I'm not sure why it chokes here.
You might want to check out the Supplement of the RosettaMP paper which contains an example of combining RosettaMP with ligand docking, and see in which order things are done there. You might have to remove the ligand before adding the membrane residue and then add the ligand back in - not quite sure.
And yes, correct - you are the first person to try this.
Good luck!
Thank you for your response, it seems that the solution was to use the AddMPLigandMover after building the membrane residue, and ensuring that ligands are in a different chain to the protein. This now runs without any errors!