I downloaded the Doom mod from here and it installed fine, I have kaspersky running and it found no malware!
http://www.moddb.com/mods/brutal-doom-64/downloads/brutal-doom-64-version-10
You will have to temporarily disable your antivirus until you get it installed.
Once installed you will have a folder called "Brutal_Doom_64_V2"
Now you need a doom 2 wad file which you can download form here.
http://www.pc-freak.net/blog/doom-1-doom-2-doom-3-game-wad-files-for-download-playing-doom-on-debian-linux-via-freedoom-open-source-doom-engine/
Just copy the doom2 wad file into your "Brutal_Doom_64_V2" folder and your done.
Now click "bd64.exe" inside the folder to run the game.