no!
The Alien wad is just an extention to DOOM 1 or DOOM 2..
So you HAVE to put at least one original DOOM wad in the folder (western doom, twilight and final fantasy 3 are total conversions -> complete games)
so you have to check out which doom version alien doom uses and then you have to put in aliendoom.wad and DOOMx.wad in GAME/DOOM
then you can select the game and the wad in GPDOOM