I have pairs of amino acids from an interface and i want a refined docking. How do i specify these restraints for pairings in haddock? i.e. create a
AIR restraint file
an input it
You can define a distance restraint between those two residues and upload it as unambiguous restraints
assign (segid A and resid 100) (segid B and resid 200) 2.0 2.0 0.0
This will define a distance restraint between residue 100 of chain A and residue 200 of chain B.
The upper limit is 2A in this case, which will enforce some atom contacts should be made.