In Warzone 2100, a weapon's damage-per-shot (and by extension, its damage-per-second) is determined by the following formula:
Base Damage = Weapon Damage-per-shot after Upgrades X Weapon Modifier
and
Damage = Base Damage - Armor after Upgrades
or
Damage = Base Damage / 3
or
Damage = 1
whichever is higher