I am doing protein-protein docking. To limit myself to a particular docking site I use the following site constraint:
SiteConstraint CA 521A S FLAT_HARMONIC 0 1 5
This works perfectly fine, and I’m getting poses only around the residue 521A.
Later on, I decided to restrict my poses to only the ones that have a particular
aminoacid contact between chain A and S. I changed the constraint file to:
AtomPair CA 521A CA 13S HARMONIC 6.23 2.0
what I’m getting now is the following error message:
error in constraint (no such atom in pose!) AtomPair 521 218795944098 218795944098 func: 13S
It looks like Rosetta has drifted away from AtomPairConstraint (that error message is not associated with AtomPairConstraint). I think whichever format Rosetta is trying to use disallows the chain designator. Which constraint file format are you using (attach the file as .txt?) Are you intentionally using the NMR NamedAtomPairConstraint?