The following example shows
how to restrain a subset (in this case
the 
atoms) of
the coordinates in ``file1" to the coordinates in ``file2":
coordinates @file1 coordinates disposition=reference @file2 vector do ( harmonic=20.0 ) ( name ca ) vector do ( harmonic=0.0 ) ( not name ca ) restraints harmonic exponent=2 end flags include harm endThis sequence of statements can be inserted anywhere after the molecular structure is defined. Note that the FLAGs statement is actually not needed, because the restraints statement has the HARM flag already turned on.