In this work, we define a "PDB topology" or "PDB file" as a specification of 1) atomic elements, 2) coordinates, and 3) connectivity of all particles. Current OpenFF tools are specifically designed to handle the PDB format, since most molecular generation and analysis tools support PDB files as output, but the algorithms and workflow presented hold in general as long as these three pieces of information are provided. The last requirement of connectivity is not always provided in PDB of systems such as proteins and RNA, as most biophysically-oriented simulation software has tools for reconstructing the connectivity for standard proteins and nucleic acids, though the information is usually provided for more general chemistries. As we will see, specification of connectivity is vital for properly interpreting structural files chemically, and must be generated in some manner.