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I'm not sure if my calculations for limiting current on Allegro's 4988 are correct. I have a 12v stepper motor with a current draw of 2A per fase.

I want just a 1.6A draw so my calculations for Vref are Vref= 1.6*8*0.1=1.28v The RS of the driver is R100 =0.1ohm.

Are my calculations correct? enter image description here

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Your calculation is correct, with 0.1 Ohms sense resistors requiring a 1.25 V reference voltage.

The absolute maximum sense(1,2) voltage is 0.5 V and you are only using 0.16 V of that range at full scale (so DAC step size around 10 mV).
This seems a little low, and I'd be tempted to increase the sense resistors to 0.2 Ohm, which uses 0.32 V full scale and increases step size to 20 mV and the reference to 2.56 V.
You could use either a simple voltage divider from your MCU VCC or something like an TL431/TLVH431 if you want the lowest noise possible on Vref.

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