I am running snugdock for Antigen-Antibody docking. As I can see from the output pdb files, the loops are moving during docking. After reading snugdock paper I do see the reason for that.
But in my case, I would like to fix the backbone of both Antigen and Antibody (for loops and nonloop regions).
I tried to include "-relax:bb_move false" flag, but it seems like it is doing nothing.
does anyone know how to fix the backbone during snugdock docking?