I moved your posting to the Cura section, because your posted in Firmware.
But Cura has some Prusa profiles and they work out of the box. I did a test with my Prusa and Cura and had no problems.
Are you sure you have selected the correct profile in Cura?
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P3D 46
Firstly, one word of advice, you probably have much better chances of someone being able to help you with your problem if you post it in a Prusa Forum, not the Ultimaker Forum.
Secondly: Are you sure the motor is wired/plugged in correctly? Sounds like a hardware issue to me...
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