Probably the easiest way is with the score application. Simply give a reference structure with “-in:file:native” and one or more structures to compare with “-in:file:s”. The score output should have a column for the C-alpha rmsd of the structure to the “native” structure.
(By the way, I’ll emphasize that you really do need the structures to be of the same protein, more or less. To get the rmsd, the score application does a strict 1:1 mapping of the residues to each other – extra or missing residues mean that things no longer line up and the rmsd you get back is meaningless.)
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