Treat it the same as any weapon. If someone is in no armour, they take DMG 3. If they are in PV2 armour they take DMG3 - (PV2 - (-4)) = 0 damage.
The coding is designed so that if you have any armour you'll just get hit by bruising damage, but no wound. If however you're wearing nothing, then expect a broken limb.
Stormers, Necanthropes and Shaktar are considered to have PV1 when attacked by a Gauss Rifle (ie: it does no damage against them except through bonus damage from a high hit score of 20+)