First thing to do in troubleshooting is reduce the variables and proceed in small steps.
Use the A4988 without connecting the Due (other than for 5V), connecting a pull-up and push button
to the step pin, so you can test the A4988 in isolation.
Get that working first. Once that's working you know the driver and motor is working.
If you have a known good stepper motor, use that first, then move to the problem motor,
so you can tell if its driver or motor.
Note its vital to set the current limit on the A4988 to roughly the right value for each motor,
too much current may burn out the driver (from experience on the Pololu DRV8825 modules
its perfectly possible to select self-destruct levels of current!).
Secondly make sure the Due pins are working by driving an LED (with 1k series resistor)
from the pins you are going to use.
Then connecting the Due and A4988 together is pretty much guaranteed to work, as you've
proved each separately.