It's not something I've seen before, and it's not clear what the issue is. A bug? A user input error?

I looked at cmap_prm.txt and it wasn't clear to me if these were two adjacent dihedrals, how they overlapped, and if the atom sequences were in the correct order.

Try a simpler test case, with only the ligand; start with just one, then two, and three, and see where it breaks down.

Rick Venable
computational chemist