I'm trying to dock a peptide (35 aa) to a trimeric receptor (P2X4, pdb: 3I5D). I need that these three subunits behaved as a single unit, without a jump, and peptide was docked to this assembly.
But I probably misunderstand how to setup a docking fold tree: constructs like dock_prot.setup_foldtree(p, "T_ABC") or dock_prot.setup_foldtree(p, "ABC_T") don't work since I have monomers (A, B, C) moving as well as the peptide (T).
The fold tree looks as following:
FOLD_TREE EDGE 1 324 -1 EDGE 324 325 1 EDGE 325 332 -1 EDGE 332 333 2 EDGE 333 660 -1 EDGE 660 661 3 EDGE 661 985 -1 EDGE 985 986 4 EDGE 986 1012 -1
What do I have to do to have this done & start docking with all three (A, B, C) subunits not moving?
Actually, solution was simple: I did not use DockingProtocol() at all, instead of it I made fold tree manually, the first edge of which covered all three subunits:
ft = FoldTree()
ft.add_edge(1,977,-1)
ft.add_edge(977,978,1)
ft.add_edge(978,1012,-1)
pose.fold_tree(ft)