Cuby input files (and the config file and some data files) are in YAML format, a human-readable and editable structured data format (YAML homepage). But don't worry. Writing YAML is easy. In most cases, the input file consist just of lines like this:
Some more details and advice on YAML
The basic format for molecular geometry. PDB format should be used where additional information on atom types and residues is required (e.g. MM calculations).
Cuby uses standard PDB format. In addition, it can use pdb-like files that use more decimals for the coordinates. This difference is autodetected on input. Such a files can not be, however, read by other programs reading the file using fixed column width.
Cuby uses z-matrix format that can use either direct input of values or named variables. Numerical values and variables can also be mixed. The block of variables is separated from the z-matrix itself by a blank line.