I’m surprised you’re not getting an error message.
One key point is that Rosetta has two major modes – fullatom and centroid. Full atom is with all the atoms, whereas centroid mode uses a reduced sidechain representation and a united-atom backbone model. Most protocols use fullatom, but things doing major rearrangements, like loop modeling and docking, often have stages where they run in the simpler centroid mode to speed things up.
The -constraints:cst_file sets the *centroid* mode constraints. Not only is the given file only active in centroid mode, because it’s centroid, it doesn’t have any sidechain atoms like OG1 and NE2 to constrain. What you want is to use the fullatom constraint file flag, -constraints:cst_fa_file. Keep in mind, though, that that file will only be active during the fullatom refinement stage. It won’t apply during the coarse centroid sampling. I would recommend making another constraint file for centroid mode, based off of the CA distances, and pass that to the -constraints:cst_file option along with the sidechain atom constraint file passed to the -constraints:cst_fa_file option.
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