The Atomic Edition works for me, I put duke3d.gpe, duke3d.grp and duke3d.cfg in the same directory
and defs.con, user.con and game.con files in the confiles subdir.
Plutonia and TNT wads work fine with prboom and I'm just trying some Quake mods, I played them only few minutes,
Hipnotic, Jaws...