DearAll
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
cheers
jonas
You can define a distance restraint between those two residues and upload it as unambiguous restraints
E.g.
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.
See also: https://www.bonvinlab.org/software/bpg/restraints/#unambiguous-interaction-restraints