The zoning scheme for a large-scale fuel-energy system involving the natural gas wells and pipelines network can be made owing to the calculation of seismic gradient models coupled with modeling of a geographic cover of the being investigated land. This will give a possibility to outline places where the system functioning can be under risk because of the particular deep structure of the geological medium. On the other hand, such zoning can reveal the distinctive feature of subarea containing the gas deposit. The comparison of the results given by a novel algorithm and the basic technique of the gradient model computing is presented here