I read the paper Rosetta and the Design of Ligand Binding Sites
and it enlightens me.
According to the method of this paper, I design my enzyme.
However, I find these are a few unreasonable results which show reaction atom of ligand do not close to catalytic triad,
but the opposite side of ligand close to catalytic triad.
So I want to make docking with constraints.
I think it can achieved with ConstraintSetMover, but do not understand how write the Constraint File.
For example, I want to set the distance betweent atom CA of resid 516 (one of catalytic triad) and C1 of ligand, and the distance is 3 ± 0.5 A .
AtomPair 516 CA 585 C1 HARMONIC Func_Def
I read the equation f(x)=[(x-x0)/sd] ^2 , but I do not konw how to set 3 ± 0.5 A in HARMONIC function.
I think " AtomPair 516 CA 585 C1 HARMONIC 3 0.5 " is wrong
Could give a right sample that how to set distance (3 ± 0.5 A)?