From Jacobson Lab Wiki
Control Files contain a sequence of plop commands to be executed. It is either interpreted by the executable or accepted as input.
Example (allowing for either option):
#!/home/jane/plop/plop datadirectory /home/jane/plop/data file logfile janes_plop_job.log energy parameters solvent vacuum # this comment will be ignored, as will the following command #load pdb /home/jane/old_pdb_files/protein.pdb load pdb /home/jane/pdb_files/protein.pdb minimize residues all residues verbose yes write pdb protein_minimized.pdb