I am using the FastDesign protocol in RosettaScripts to design some residues in the neighborhood of a ligand, specifically with constraints of N-O pair distance for NAD binding.
I've added constraints for the two N-O pairs to be 3.0 and 3.3 angstroms each with harmonic function and sd of 0.5, but somehow the distances are not kept below ~4.0 at all. (I've just observed a structure with over 6.0 angstrom distances for the two pairs.
I'm using talaris2014 score function and added a line in the xml file to re-weight atom_pair_constraint with a value of 1.0.
Is there something obvious that I'm missing?
From what you're saying, I can't see anything obviously wrong. That said, a lot may depend on the particulars. How are you adding the constraints? How are they getting used?
If you could post the XML and constraint files you're using, that may help to debug what's going on.