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make sure when you make the dmg formula that it includes defence. such as "a.mat - (b.mdf * 0.5)" where before it deals dmg it take into account for def.

I've done it before but when the character reach a certain level low level enemies always give 0 dmg to my party.

try turning down the defense they will get along the way, say if at endgame they would have 200 try seeing if 150 would work.