Here the input model is a RNA structure obtained from the PDB. The nomenclature used for residue names and some atom names is significantly different from that used in CNS. There is a utility program called fix_dna_rna which can be used to convert a PDB format DNA/RNA file to something more suitable for CNS:
fix_dna_rna < 157D.pdb > 157D_fix.pdb [1 second]
The fixed coordinates of the model must be converted to a format suitable for use in CNS and a file describing the molecular topology of the model (MTF file) must also be generated. This is done with the CNS task file generate_easy.inp or for more complex cases with generate.inp.
cns_solve < generate_easy.inp > generate_easy.out [7 seconds]
The ribose sugars in the CNS nucleic acid topology files are in the oxy form (ie. RNA) so no patches need to be applied.
There are two files generated: a PDB file and an MTF file (this contains the molecular topology information which describes to covalent topology of the molecule).