DNA polymorphism: a comparison of force fields for nucleic acids.
The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)(2) in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies.
Reddy
Swarnalatha Y
SY
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
Leclerc
Fabrice
F
Karplus
Martin
M
D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009038:Motion; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011110:Polymorphism, Genetic; D018807:Polymorphism, Single-Stranded Conformational; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012996:Solutions / Q000737:chemistry; D055672:Static Electricity; D013314:Stress, Mechanical; D014867:Water / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D012996:Solutions; D014867:Water; D004247:DNA