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I have an arduino motor shield r3 being used by a arduino uno. I'm running a 12 volt stepper motor that is attached to a 32 to 1 gear reducer. I have the Vin pin removed and powering it with a 12 volt power supply. After a few minutes of use of the stepper doing 2600 steps one way then 2600 steps the other way the shield starts to mess up and act like it can't handle the motor. The main chip on the board after the few minutes of running is very hot, I actually burnt my finger slightly from just touching it for a second. Is there any thing that could be wired wrong to cause this, such as the stepper not being wired right? Or could it be the stepper motor and gear reducer is just too much work on the shield? Any suggestion what could be wrong would be very helpful thank you.
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Do you know the specs of the motor?
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I'm not sure what all you want too know about it specs wise so here is the link to the one I bought.
http://www.ebay.com/itm/Stepper-motor-NEW-Nema17-DIY-CNC-Router-Mill-Robot-Reprap-Makerbot-Arduino-/320842713273?pt=LH_DefaultDomain_0&hash=item4ab3b748b9
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I have an arduino motor shield r3 being used by a arduino uno. I'm running a 12 volt stepper motor that is attached to a 32 to 1 gear reducer. I have the Vin pin removed and powering it with a 12 volt power supply. After a few minutes of use of the stepper doing 2600 steps one way then 2600 steps the other way the shield starts to mess up and act like it can't handle the motor. The main chip on the board after the few minutes of running is very hot, I actually burnt my finger slightly from just touching it for a second. Is there any thing that could be wired wrong to cause this, such as the stepper not being wired right? Or could it be the stepper motor and gear reducer is just too much work on the shield? Any suggestion what could be wrong would be very helpful thank you.

Without knowing the power draw of the stepper motor, there's nothing to compare to the motor controller's capacity. The listing on eBay does not talk about the power draw, either. It's quite possible the motor draws more power than the controller can deal with without additional heat sinking.

Get some thermal glue/paste and a good IC heat sink, and put the sink on the chip. That will cool it right down. And if it doesn't, then add a fan blowing across it :-)
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If you have a meter you could measure the resistance of the coils and the voltage you are using to use Ohms law to give you an idea of the current the motors are using and compare it with the spec of the motor driver IC.

Martyn.
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Its not a good idea buying a motor without any specifications like this - you have no way of complaining if its the wrong motor....

Usually stepper motors come with these specifications as a minimum:

max current for one winding, winding resistance (or voltage at rated current), winding inductance, holding torque at rated current, number of steps, moment-of-inertia of rotor.

We crucially need to know the first two, current + resistance (too much current can damage the motor thermally or magnetically).  winding voltage and resistance are related to current so either will do.  Resistance is easy to measure, rated current you will have to guess.
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