AMBER (Assisted Model Building with Energy Refinement) is a force field that allows for the simulation of proteins. Basic proteins were folded by a Monte-Carlo algorithm parameterized by AMBER on MATLAB. Simulations exhibited self-organized critical (SOC) behavior and are shown to be stable throughout the simulations by use of pairwise distance matrixes. Frequency shifting is explored as a possible explanation of the mechanisms behind structure inducing probes (SIPs) in the solid phase synthesis of proteins. This also provides a mechanistic link to many other SOC systems
