I'm trying to model a structure with NAD in. Before, The program ran well without NAD. And when I was using MODELLER 4, it ran well even with NAD. But I've installed MODELLER6v1 this time, I've changed the letter that stands for NAD as "J", and "SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = on, HETATM_IO = on", get-model.log kept telling me that:
r_stere_604E> Torsions must have periodicity 1,2,3,4,5,6: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Would anybody tell me what does that mean and what I should do to avoid this error? Thank you very much.