We analyzed the accuracy of the fragment molecular orbital method using various representations of the embedding potential and extended its applicability to large basis sets by proposing to use potential-derived point charges with screening combined with the adaptive frozen orbital treatment of the detached bonds A comprehensive set of basis sets: STO-3G, 6-31G*, 6-311G*, 6-31++G**, 6-311++G**, cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, and aug-cc-pVTZ was employed, for tests systems we used water clusters with 16 and 32 molecules, the a-helices and beta-strands of alanine containing 10 and 20 residues, as well as chignolin (PDB, IUAO) and Trp-cage miniprotein (PDB, IL2Y)