The error indicates you have a non-matching atom type set and score function. The warnings suggest you probably have full-atom poses that you are trying to read in to a protocol that expects centroid poses (because it is rejecting sidechain heavy atoms). Try a flag to indicate you want full atom poses, like in::file::fullatom, or maybe the other way around, a flag that forces it to convert inputs to centroid?
Which executeable is this? Are you trying to do fullatom or centroid?