In response to user requests, I have created a MODELLER file archive, from where you can download example TOP scripts. I will be adding examples to this archive on an occasional basis, some of which will probably find their way into future releases of MODELLER. Of course, it wouldn't be much use without user-contributed examples; there are instructions on the page on how to send example files to me for inclusion.

You can find the archive at: http://salilab.org/modeller/archive.shtml

Enjoy!

Ben Webb, Modeller Caretaker