A modification of the GADGET-2 program package is proposed for three-dimensional modelling of gasdynamic flows in protoplanetary disks when perturbing objects (components of a binary system, brown dwarfs, protoplanets) are present. In these systems, the matter in the common disk falls onto the central star and companions to form accretion disks around them. The GADGET-2 code has been supplemented for calculating the accretion rate to each massive object and the line density of matter in the direction toward the central star as functions of the phase of the orbital period. The orbital parameters of the companion are specified as initial conditions for the problem. These orbits can be circular, eccentric, or inclined relative to the plane of the disk. With the aid of the modified code, details in the inner parts of the disk can be calculated with high accuracy: the accretion disks of the star and the companion are identified, as well as the gas bridge between them, flows of matter from the common disk which fill the accretion disks with matter, and density waves in the accretion and common disks.