rmcgibbo/mdtraj — pull request #430 by swails (2014-05-01 16:09:32+00:00)
Title: Associate .parm7 extension with Amber prmtop

".prmtop" is a rather antiquated extension for Amber. Most programs these days use ".parm7" (including VMD, etc.). I would say that ".prmtop" is more standard for _old_-style topology files (pre-Amber 7, from back in the late 1700s). While old-style topology files can still be created and used for explicit solvent calculations, they're rare.

If you want to be able to read old-style topologies, though, the `AmberParm` class from ParmEd can do it. Probably not worth it though.