is it possible to add simple constraints in AutoDock?
Dear @Philip-0 ,
What type of constraints do you have in mind?
it would be nice to have have possibility to constrain the distance between the terminis of the ligand.
Sometimes it is nice if one does not have to load the full conformation of a bigger ligand.
With constraints one can rebuild the complex after the docking and starts MD-simulations.
one possibility might be to ask the Vina extension to compute many modes (e.g. 1000) and then use a script to filter out the conformations that do not satisfy the distance constraint. Another possibility might be to directly modify the source code of Vina to add a term to the scoring function that would penalize one or more unsatisfied constraint(s) (similar to a NMR energy function). We're going to look into this. Thanks for the suggestion.