Editing Basis set superposition error (BSSE)

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Interaction energies between two atoms or molecules A and B  are typically calculated as the energy difference between the product complex AB and its components A and B:

 Eint = E(AB,rc) - E(A,re) - E(B,re)            (1)

The label rc is used here to indicate the geometry of the product complex AB, while re indicates the geometry of the separate reactants. The interaction energies calculated according to equation (1) are often too large and lead to severe complications for systems bound through dispersion interactions or hydrogen bonds. Small basis sets stabilize the complex more than the separate components due to the basis set superposition error (BSSE). The latter is due to the fact that the wavefunction of the monomer is expanded in much less basis functions than the wavefunction of the complex. Each of the atoms has a larger number of basis functions available than in the monomer, leading to a more flexible description of the wavefunction and ultimately a lower energy. 
One obvious solution to the basis set superposition error is the use of extremely large basis sets. This is, however, hardly feasible for most of the chemically interesting systems. The second approach termed the Counterpoise Method (CP)  is an approximate method for estimating the size of the BSSE. While the description of the product complex is unchanged in the CP method, the separate components are provided with a basis set of identical size as is available to the dimer. The CP corrected interaction energy can in the simple most case then be computed as:

 Eint,cp = E(AB,rc)AB - E(A,rc)AB  - E(B,rc)AB + Edef             (2)
 with Edef = [E(A,rc) - E(A,re)] + [E(B,rc) - E(B,re)]

The superscripts AB indicate here that the complex as well as the separate components are calculated in the same absolute basis.

If using Gaussian09, they can be computed using the tool: Couterpoise, or by running the Massage keyword and setting the nuclear charge of the atoms of a fragment to 0.0 (1 Nuc 0.0) leaving behind the basis functions positioned at this centers.

http://www.gaussian.com/g_tech/g_ur/k_counterpoise.htm

For more info when using G09 [[How to compute BSSE]]

More info:

http://www.cup.uni-muenchen.de/ch/compchem/basis/bsse1.html

http://en.wikipedia.org/wiki/Basis_set_superposition_error