Im not quite sure if you are being deliberately obtuse - if your system has mass ,springs and dampers then the system equation (Newton) is the one I have mentioned. It is valid for any number of degrees of freedom and any form of excitation in either time or frequency domain.
Regardless of the software you are using it will either solve Newton's equations (which obviously involve mass) or the Lagrange method (where kinetic energy is mv^2/2, again dependent on mass).
I'm sure you can use software too bad you can't understant how it works.
How much TQ does it make though?