Is it possible to use nagtive contraints in haddock. i.e assign an energy penalty if a residue on one protein gets close to another.
Also in the webserver is it possible to assign AIR for atoms and not just residues?
Thanks in advance
Yes you can, for example by setting a minimal lower bound, e.g. 20A and defining a very large upper limit, e.g. 500A
The restraint would look like:
assign (segid A and residue XX) (segid B and residue YY) 500.0 480.0 0.0
assign (segid A and residue XX) (segid B and residue YY) 20.0 0.0 480.0
both give the same range of distance: between 20 and 500A (i.e. the minimal distance is thus 20A)
If you don’t know a specific residue in protein B, I would then modify the restraint to:
assign (segid A and residue XX) (segid B and name CA) 500.0 480.0 0.0
i.e. the second selection is only to CA atoms to limit the number of atoms selected and save computing time
As a reminder, distance restraints are defined as:
assign (selection1) (selection2) distance lower-bound correction upper-bound correction
where the lower limit for the distance is calculated as: distance minus lower-bound correction and the upper limit as: distance plus upper-bound correction.