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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?

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As you say, you can't use the CONECT records in a PDB file because it's limited to 99,999 atoms (rather, I think the first digit is treated in base 36, so 360,000 atoms).

VMD supports other file formats, and has a plugin system for you to define your own format. Of the ones listed there, your best bet is likely the Tripos mol2 file.

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