I checked many tutorials and the haddock JACS paper, but could not find a specific distance cutoff to define passive residues. I spot ‘auto_passive_radius = 6.5’ in one of the parameter files. Does haddock define passive residues as any accessible residue within 6.5 angstrom from any of the active residues? Do you use the C-beta distance/centroid distance for the calculations?
Any info would be very helpful. Thank you.
Indeed the server uses a 6.5A Distance cutoff between any heavy atoms of two residues
Thank you very much.