Chem-Bio Informatics Journal
Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation
Fragment molecular orbital (FMO) calculations were performed for explicitly solvated single-stranded DNA (ssDNA), ssDNA binding protein, and their complex in order to assess the solvent effects on the solutes and thereby to find optimal solvation conditions for FMO calculation. A series of solvated structures were generated with different solvent thicknesses. The structures were subjected to FMO calculation at MP2/6-31G* to obtain the net charges and internal energies of the solutes and the solute–solvent interaction energies as functions of the solvent thickness. In all cases, the properties showed complete or marginal convergence at ca. 6 Ǻ, regardless whether or not the system charge was neutralized. This suggested that the first and second solvent shells mainly determine the electronic structure of a solute while the outer solvent including ions has only minor effects, consistent with several preceding reports. In light of this, and considering safety as a factor, we conclude that a solvent shell thickness of ca. 8 Ǻ suffices for FMO calculation of the solutes.