Abstract
Applicability of five popular force fields (AMBER, CFF91, CVFF CHARMM and GROMOS) to the structural analysis of nucleic acids without explicit solvent has been examined. Structures of nine deoxyoligonucleotides in the A- and B-forms were optimized by energy minimization and compared with well-refined crystallographic data. Several models for electrostatic interactions were tested including constant and distance dependent dielectric functions in combination with varied effective charges of the phosphate groups. Similarity tests of the theoretical and experimental structures were based on a distance analysis in a conformational parameter space of the DNA molecules and on a proposed scoring scheme.
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