Yes. The simulation will not be what you think. You have forced CHARMM to neglect a serious error (bomlev -2). NEVER RUN A CALCULATTION THAT REQUIRES YOU TO CHANGE THE DEFAULT BOMLEV (unless you really know what your are doing) At the very least some atoms will NOT be subject to the sbound force.
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden