List of file formats
GROMACS structure file format format (specification, Wikipedia).
Protein Data Bank (PDB) file format (specification, Wikipedia) is the format used for storing three-dimensional structures of proteins, nucleic acids, and complex assemblies in Protein Data Bank.
XYZ file format (specification, Wikipedia) is simple format for storing types and positions of atoms in three-dimensional Cartesian space.
CCL: SUMMARY: Some Molecular File Format Descriptions