The time evolution of a system of two protoplanets still embedded in a protoplanetary disk has been studied viscous hydrodynamical simulations. Resonant capture of the planets is seen, where the order of the resonance depends on the initial spatial separation of the planets, and the properties of the disk and the planets. Resonant capture leads to a rise in the eccentricity and to an alignment of the spatial orientation of orbits. The numerical results are compared with the observed planetary systems in mean motion resonance (GJ~876, HD~82943, and 55~Cnc). We find that the forcing together of two planets by their parent disk produces resonant configurations similar to those observed, but that eccentricity damping greater than that obtained in our hydrodynamic simulations is required to match the GJ~876 observations.