The recently developed ab initio many-body theory of positron molecule binding [22J. Hofierka et al., Many-body theory of positron binding to polyatomic molecules, Nature (London) 606, 688 (2022)NATUAS0028-083610.1038/s41586-022-04703-3] is combined with the shifted pseudostates method [A. R. Swann and G. F. Gribakin, Model-potential calculations of positron binding, scattering, and annihilation for atoms and small molecules using a Gaussian basis, Phys. Rev. A 101, 022702 (2020)PLRAAN2469-992610.1103/PhysRevA.101.022702] to calculate positron scattering and annihilation rates on small molecules, namely H_{2}, N_{2}, and CH_{4}. The important effects of positron-molecule correlations are delineated. The method provides uniformly good results for annihilation rates on all the targets, from the simplest (H_{2}, for which only a sole previous calculation agrees with experiment), to larger targets, where high-quality calculations have not been available.