The integrated framework consisting of TOPICS, VMEC and FORTEC-3D, has been applied to provide an estimate of the neoclassical toroidal viscosity (NTV) produced by the applied magnetic perturbations (MPs). Six picture-frame error field correction coils in each row in JT-60SA realize the various patterns of the applied magnetic field spectrum. The NTV is investigated for various toroidal phase differences. As long as the same coil current is applied, the n = 3 MPs generate the same NTV, regardless of even or odd parity, or energizing the middle coils or not. The n = 1 MPs give rise to larger NTV than the n = 3 ones. The NTV invoked by the n = 1 resonant MPs is virtually equivalent to that by the n = 1 nonresonant MPs with five-fold coil current.