We develop nonorthogonal projectors, called Lowdin projectors, to construct an effective donor-acceptor system composed of localized donor (D) and acceptor (A) states of a long-distance electron transfer problem. When these states have a nonvanishing overlap with the bridge states these projectors are non-Hermitian and there are various possible effective two-level systems that can be built. We show how these can be constructed directly from the Schrodinger or Dyson equation projected onto the D-A subspace of the Hilbert space and explore these equations to determine the connection between Hamiltonian and Green function partitioning. We illustrate the use of these effective two-level systems in estimating the electron transfer rate in the context of a simple electron transfer model. (C) 2004 American Institute of Physics.