Hi Everyone
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
MIke
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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
or
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.
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