I want to know what are the criteria used by pyrosetta in detecting a hydrogen bond. If anybody can guide me to a ref., it will be more useful.
Here is the original paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC406446/
Depending on the version of PyRosetta your using, the potential is slightly different. I don't know the exact details, but I believe the geometries have been refit among other things. The switch was pulled to use these changes as default somewhere between may 30th and June 4th. So, if you have a PyRosetta version from after that, it will be updated to use this (And so you know, these changes correspond to the talaris2013 energy function, which is replacing standard + score12 - there are more changes than just the Hbond updates that were also flipped to default). I know the guys who worked on this are working on a paper, but I could see if they could give you more information on the changes.
In addition, if you want to restore the defaults from before, you will need to pass PyRosetta this option: -restore_pre_talaris_2013_behavior