# This reads in the template pdb file and thus allows us to use the @nonhydrogens
# special group later in the input
MOLINFO STRUCTURE=beta-hairpin.pdb MOLTYPE=protein

# This stores the positions of all the nonhydrogen atoms for later analysis
cc: COLLECT_FRAMES ATOMS=@nonhydrogens

# This should output the atomic positions for the frames that were collected to a pdb file called traj.pdb
OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=cc FILE=traj.pdb
