I read a single-residue pose stored in pdb file with “pose_from_pdb”. Rosetta automatically added the terminus (OXT and two hydrogen atoms). Is there any way to prevent terminus adding or popping them off after reading in?
It is not possible to prevent them from being read in. It should be fairly straightforward to remove them. I believe the function name is something like core::chemical::util::remove_terminus_variant_from_pose_residue. If you can’t find it let me know and I’ll go look again and find out for sure.