Consult on the submiting format of PNAS
The author instructions state that "A single PDF file is acceptable for initial submissions of all research articles except Contributed papers". Further down it is also stated that "Publication-ready file formats include Word or LaTeX."

This means that depending on what type of manuscript you are submitting, different rules may apply. Word and LaTeX (the latter must be accompanied by a PDF file) are fine but for a few forms like their "Express Submissions" require a single pdf to be submitted initially. Only of the manuscript passes the initial stage will it be required to provide editable files.

You should generate the PDF from your Word document or LaTeX class files according to the instructions.