The arduino is capable of producing the pulse sequences you need but without more info we cannot be sure what sequence the pulses need producing in, the current is being drawn by the motor and what other components will/may be needed.
Also, keep in mind that offical Arduinos, and all third-party versions I'm aware of, can only generate PWM signals of the same voltage level as what is powering the microcontroller chip. Therefore on a standard Uno, Mega, or Leonardo, while a constant 3.3 VDC
is available the PWM always be at 5 VDC
. Therefore, you will have to reduce the voltage of the PWM some how, either by a voltage divider or a uni-directional level shifter circuit.