Hi! 
I installed MGS2 Substance (the GOG version on my LMDE 6 computer) using the option “Installs the GOG version with V’s Fix” from the lutris website.
The installation went smoothly however once in game the triggers of my xbox360 gamepad weren’t working and those are pretty much necessary since they are needed to change/use items and weapons.
I searched around for a bit trying to find a solution but there were none as far as i could tell. So i found out that there is a program called “AntiMicroX” that will allow the user to rebind any keyboard keys to the controller. All you need to do is to rebind the keypad number 7 and 9 to LT (numpad 7) and RT (numpad 9). Just save the program profile as “mgs2” or something and run it before you start the game.
Now the triggers are working fine as the item/weapon buttons!
Hope this is some useful info for people out there stuck as i was! 