Prabhu Ninad V, Panda Manoranjan, Yang Qingyi, Sharp Kim A
Schering-Plough, Kenilworth, NJ, USA.
J Comput Chem. 2008 May;29(7):1113-30. doi: 10.1002/jcc.20874.
An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined.
开发了一种用于分子动力学的显式离子、隐式水溶剂模型，并通过DNA和RNA模拟进行了测试。隐式水模型使用有限差分泊松（FDP）模型，并采用了OpenEye ZAP库中实现的平滑介电常数方法。显式抗衡离子、共离子和核酸采用朗之万动力学分子动力学算法进行处理。当靠近溶质时，离子静电作用在FDP模型内处理；当远离溶质时，采用库仑模型处理。两区模型减少了计算时间，但保留了对溶质附近离子气氛静电作用的精确处理。可以设置离子组成以再现特定的离子强度。整个离子/水处理与分子动力学软件包CHARMM接口。使用CHARMM-ZAPI软件组合，对A和B型双链DNA以及四环RNA进行了隐式溶剂模型测试，得到了稳定的模拟结果，其结构与实验结果相近。该模型还再现了A到B双链DNA的转变。还研究了离子强度的影响以及B型双链DNA周围抗衡离子气氛的结构。
