I'm using rosetta mini 3.1 fixbb and is trying to interpret the residual scores in the pdb file output. The total score seems to be the sum of the terms in the line starting with 'pose' which seems to be the sum of the contributions from each residue listed below. The term hbond_sr_bb and hbond_lr_bb does not have residual contributions (all zero) but is nonzero in the pose line. Is this a bug or is there a reason why these term doesn't have residual contributions listed?
There is a reason for this - it is not a bug. The way the hydrogen bonds are calculated, storing those values on a per-residue basis requires a bunch of extra effort beyond just calculating the energies. In other words, the hydrogen bond energies are accurate, but storing them on a per-residue basis requires extra work (slowing the program down). So, they're stored only on a whole-pose basis.
If you want to fix this, there's a demonstration of how in the backrub app. You'll need to do some coding of your own. You need to use the function decompose_bb_hb_into_pair_energies; look at backrub.cc line 263 for an example. In fixbb.cc, you'll have to make a ScoreFunction, make an EnergyMethodOptions, use the function, and pass the ScoreFunction into the PackRotamersMover.