We carry out quantum inelastic scattering calculations of collisions of Rb atoms with inverting NH3 and ND3 molecules in the energy range between 0 and 100 cm−1, which are important for experiments using velocity-controlled molecular beams to probe scattering resonances. We focus on molecules initially in the upper level of the ammonia inversion doublet for j=1, k=1, which is low-field seeking and can be controlled in a Stark decelerator. We calculate the integral elastic and state-to-state inelastic cross sections in the coupled-states approximation. We demonstrate the presence of both shape and Feshbach resonances in the elastic and inelastic cross sections at low collision energies and discuss their origin in terms of the bound states of the Rb-ND3 complex. We also consider elastic and inelastic cross sections in the ultracold regime, using close-coupling calculations, in order to assess the viability of sympathetic cooling of ND3 by Rb. The inelastic cross section for relaxation to the lower level of the inversion doublet is smaller than expected for such a strongly coupled system but is still likely to be too large to allow sympathetic cooling for ND3 in low-field-seeking states. However, there is a good prospect that sympathetic cooling will be possible for molecules in high-field-seeking states even when the collision partner is a magnetically trapped atom in a low-field-seeking state
