A method for estimating pressures at a gas engine using a real-time model-based observer is implemented by a pressure estimation computing device. The method includes receiving a design schema describing an intake manifold and a plurality of components associated with the gas engine, segmenting the design schema into a plurality of segments defining a plurality of sections of the gas engine, defining a fluid dynamics model associated with each of the plurality of segments, defining a plurality of interconnected elements based on the plurality of fluid dynamics models, receiving at least one pressure measurement from at least one of a plurality of sensors associated with each of the sections of the gas engine, estimating a plurality of pressure values at each section of the gas engine, and controlling fuel injection to at least one gas cylinder based on the estimated plurality of pressure values.