Having just mentioned it in the context of making publication-quality pretty pictures, another brief note thanks to a citation request on the NanoEngineer Development/User Group (groups.google.com/group/nanoengineer-dev).
There's a website hosted at bionano.physics.illinois.edu for the conversion of NE-1 DNA mmp files to all-atom pdb ("Molecular Dynamics Simulation of Custom DNA Nanostructures Created by NanoEngineer-1") and NE-1's FNANO08 proceedings article ("NanoEngineer-1 – A CAD-based molecular modeling program for structural DNA nanotechnology") was included (with thanks to its use by German Barcenas) in the recent International Journal Of Molecular Sciences article "Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions."
The bionano site is a dramatic improvement from the NAMOT + sed'ing I worked up many years ago while getting something DNA-related stood up.
As a still-not-irregular user myself, I can appreciate the small hurdles needed to keep the program upright in modern OSs (or the need to just run VirtualBox and be done with it) – therefore noting both Bryan Bishop's dev page (worth the visit to github for the preserved gallery alone!) and Bruce Allen's Molecular Dynamics Studio effort and sourceforge-available download.