Hello --
You can use the "write atompot" ELEC command (http://www.poissonboltzmann.org/docs/apbs-overview/#elec) to do this. You will need to write out the atom potentials for two calculations: the system of interest and a reference system (e.g., with uniform dielectric) with the same coordinates. Subtracting the results of these calculations and multiplying by the atomic charges should give you the energies you're requesting.
Thanks,
Nathan