Example mapping and bond definition files are present in the ``test/data`` directory. Their format is explained below.
After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created. The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided. The itp file contains the parameters for each molecule type. **NB**: charges are not currently set by PyCGTOOL as MARTINI only allows charges on certain bead types.
Mapping / Bond Definition Files
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The mapping and bond definition input files use a format similar to the GROMACS itp/top format.