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)?
Since you found the harmonic equation I assume you found the constraints doc page: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file
You can't set a "range" of 3 +- 0.5 with harmonic. It's a parabola, it doesn't have a range, it is defined over all possible X. You can play with the SD parameter such that the parabola is narrower or wider, which will have the effect of disfavoring / being permissive of distances further from 3 angstrom, but you can't forbid values outside the 2.5-3.5 range.
Square well functions don't work terribly well with Rosetta because they are unminimizable, but reading the doc page I do see FADE which may be of some use. Find FADE on the page and see if meets your needs better?
I always encourage people to plot out constraint energy value vs. x deviation in the plotting software of their choice to get a feel for how strong a constraint they are creating. Remember that "good residues" are in the range of -3 to -2 energy units.
Thanks for your suggestion.
Function of constraint energy is complicated.
I will have a try ~~
If you're looking to do something like a harmonic function, but have a range (instead of a point) which has a zero value, I'd recommend the FLAT_HARMONIC function.
This will allow you to set a range where the constraint will have no penalty, and then you'll get a harmonic penalty for any deviation outside that range. Depending on how stringently you set your sd value, you can get something rather close to a "square well" function. (But as mentioned, that's probably not necessary. You don't need much of a penalty to keep Rosetta from sampling it.)