The fragment molecular orbital (FMO) method was combined with the second order Moller-Plesset (MP2) perturbation theory. The accuracy of the method using the 6-31G* basis set was tested on (H2O)(n), n=16,32,64; alpha-helices and beta-strands of alanine n-mers, n=10,20,40; as well as on (H2O)(n), n=16,32,64 using the 6-31++G** basis set. Relative to the regular MP2 results that could be afforded, the FMO2-MP2 error in the correlation energy did not exceed 0.003 a.u., the error in the correlation energy gradient did not exceed 0.000 05 a.u./bohr and the error in the correlation contribution to dipole moment did not exceed 0.03 debye. An approximation reducing computational load based on fragment separation was introduced and tested. The FMO2-MP2 method demonstrated nearly linear scaling and drastically reduced the memory requirements of the regular MP2, making possible calculations with several thousands basis functions using small Pentium clusters. As an example, (H2O)(64) with the 6-31++G** basis set (1920 basis functions) can be run in 1 Gbyte RAM and it took 136 s on a 40-node Pentium4 cluster. (C) 2004 American Institute of Physics.