Paper Citing NAMD - Abstract
Hart, Katarina; Foloppe, Nicolas; Baker, Christopher M.; Denning, Elizabeth J.; Nilsson, Lennart; MacKerell, Alexander D., Jr.
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:348-362, JAN 2012
The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles epsilon and zeta (BI = epsilon-zeta < 0 and BII = epsilon-zeta > 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant, and accumulating evidence shows that BII affects the overall structure of DNA and thus influences protein DNA recognition. This work presents a reparainetrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75% ethanol and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.
