Elsevier

Computers & Chemistry

Volume 19, Issue 3, September 1995, Pages 253-258
Computers & Chemistry

Workshop on computational methods for large molecular systems
Applicability of commonly used atom-atom type potential energy functions in structural analysis of nucleic acids. The role of electrostatic interactions

https://doi.org/10.1016/0097-8485(95)00010-PGet rights and content

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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