I am doing side-chain packing on a fixed backbone over a discrete set of configurations. Given a set of (non-rotamer) side-chain configurations I'm using Rosetta to calculate one-body and two-body energies using the standard scoring function. I observe to things that seem strange in the two-body energies:
1) For a pair of residues sometimes the two-body energies are almost all zero except for a couple configurations. This sort of makes sense if the residues are far enough apart, but does it make sense that they are *exactly* zero?
2) For some configurations the two-body energy depends on only one of the residues and is constant w.r.t. the other. I've observed this in a small protein between Lysine and Tyrosine, but I could probably find other examples. In this case the two-body energy only varies with the Lysine side-chain.
Do these conditions sound normal or should I suspect a bug somewhere in my code?