An improved nucleic acid parameter set for the GROMOS force field.
Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson-Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves.
Soares
Thereza A
TA
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland.
Hünenberger
Philippe H
PH
Kastenholz
Mika A
MA
Kräutler
Vincent
V
Lenz
Thomas
T
Lins
Roberto D
RD
Oostenbrink
Chris
C
van Gunsteren
Wilfred F
WF
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D015246:Deoxyribonuclease EcoRI / Q000737:chemistry; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D015394:Molecular Structure; D013816:Thermodynamics
D004247:DNA; D015246:Deoxyribonuclease EcoRI