I have created a formation with AC4400CW (with custom livery from BNSF) coupled with a 6 metrolink rotem cars (being 4 coach cars and 2 cab cars one at each end) but I can't open the metrolink rotem cars doors (I think it's because the AC4400CW isn't compatible with metrolink rotem cars, right?) is there a way to bypass this and make the rotem cars doors open?
The loco you're using is a freight loco, which was never designed with the intention of operating passenger trains. Only way to get around it is opening the doors yourself.
