So the problem is this: setup.exe of Duke Nukem 3D Atomic Edition doesn't work at all. My Vista keeps claiming that it doesn't find the file. Yes, I tried "run as administrator", but still nothing. I want to open the setup to change the controls. I know that many of you are gonna say: "Change to EDuke32" but I wan't to keep the game as unmodified as possible. Any ideas how to make the setup.exe work? The actual game works fine.

Hi,
are you using the shortcut on your start menu folder ?

I'm not using any shortcuts. I go to Program Files (x89) / GOG.com / Duke Nukem 3D and then choose the setup.exe

Take a look in the game start menu folder. If there's a shortcut for the setup give it a try to see if it makes any difference.
If it still doesn't work,
-maybe try reinstalling the game outside Program Files,
-when (re)installing, right click the game installer and run it as admin instead of double clicking on it
-make sure your AV isn't interfering with the installation process

Where can I find this start menu folder?

You're welcome ;)

I am trying to get Duke Nukem Atomic edition to play. I have tried clicking setup, the shortcut icon and going into program files and clicking everything there. I am running vista and have plenty of hard drive space and memory as far as I know. I don't know what to do as I am not computer friendly

Firstly, this thread was resolved and closed so you really ought to start a new thread rather than re-open this one.
Secondly, you've not given anywhere near enough information for anyone to be able to help you. What version of Vista are you using? Is it 32-bit or 64-bit? What are the specs of your machine? CPU? RAM? GPU? Are you running the app as an administrator? Have you tried various compatibility modes? Also, why won't it run? Any error messages? Crashes? What happens, if anything?
Additionally, I recommend not using the Program Files folder as it is a protected folder and can cause issues with older software.
You might also want to use eDuke32 instead of the bundled DOSBox that GOG provides.
Also, have you raised a ticket with GOG support?

OK I didn't know that this was a closed thread because I have been a member for less than 30 days. I know little to nothing about computers other than how to click and play. I was able to get into the program files that said something about run as an administrator and the compatability mode and finally got the game to work. I have a question about cheat codes. When this game first came out a friend gave me a list of cheat codes but they don't seam to work in this version, are they still good? Do you know what they are maybe I just typed them in wrong cos it's been over 10 years since I have played this game. Thank you for you help.
Before I forget to tell you as of now I was told that I can't start a new thread yet, I guess I haven't been a member long enough.

By closed thread I was referring to the date. Before your post it was last updated 11th Feb. Also, the thread is marked as solved, so with both of these considerations this thread is closed.
If you go to the game's forum you can click on the + new topic button to create a new thread. You can also then mark it as a question so that once it has been solved you can mark it as such.
As for cheats, there are only 6 pages (with 30 titles on each page) of topics for Duke Nukem on GOG, and on the third page there is a topic called DN3D Cheat Codes. It's not hard to find, but I've put a link here for you too.
http://www.gog.com/en/forum/duke_nukem_series/dn3d_cheat_codes