I need to generate an output file from my molecular data that can be loaded into VMD to visualize the bond connectivity. I'm not sure what the best choice is. I know the PDB format has a HETATOM record with a CONECT field, but I believe this is supposed to be used only for unusual connections or very small molecules. Also, this field is limited to 5 digits, and some of my systems have > 1 million atoms.
The other option is to write two files, a PDB file with coordinate information and a PSF file with connectivity. But then I have to lug around two files everywhere, which seems unnecessary.
Is there a better format I'm missing?