Fragment molecular orbital method: application to polypeptides

Recently we have proposed the fragment molecular orbital method for calculating large molecules such as proteins. The method, with some modifications for a practical convenience, was applied to the model peptides of (Gly)n and (Ala)n (n=5–20), [Met5]enkephalin (YGGFM), and the synthetic designed peptide ALPHA-1 (acetyl-ELLKKLLEELKG). The calculated total energies compare well with those from the conventional ab initio MO method; the errors were within ∼2 kcal/mol. It indicates that the fragment MO method is sufficiently accurate and useful to study electronic properties of large molecules.