FAQ: What does “ERROR) No molecules loaded” mean?

This error message is harmless. The provided vmdrc files apply specific representations to the first molecule that is loaded into the program (i.e. proteins displayed in NewCartoon and hetero atoms as licorice). If a molecule is not loaded upon initializing VMD, either by double-clicking the PDB file or through the command line (i.e. ‘vmd 3SGJ.pdb’), the representations are not applied to anything and the program reports an error.

These messages can be ignored, and the 3D-SNFG representations should remain functional. It simply means that the representations for the input molecule will have to be created manually.