It is possible to use minrms to align nucleic acid chains (although it's not clear if this is a useful capability).
To do that, create a custom atoms_used.txt file containing the PDB codes for the atom type(s) you want to use for structure comparison. (The lines in that file must contain the name of a PDB atom type which is common to all RNA or DNA nucleic acids such as " C3'" or " C5'".) Example "atoms_used.txt" file (containing only one line):
" C3'"
In that case, the RMSD will be calculated between the positions of C3' atoms in either RNA chain. (Note: A blank space must precede the atom names on each line, eg " C3", " C5'",... The quotes (") were added above only to clarify the position of whitespace in the file and should not appear in the "atoms_used.txt" file.)
Once you have created a new "atoms_used.txt" file, run minrms using the -atoms-used atoms_used.txt and "-HS" arguments. (You must include the "-HS" argument to inform minrms that the molecules being aligned do not contain any helix or sheet secondary structure.)
Minrms has not been carefully tested when applied to RNA molecules, so please report problems to the issue tracker if these instructions do not work.