MOLECULAR DYNAMICS SIMULATIONS AND METHOD DEVELOPMENT

分子动力学模拟和方法开发

基本信息

批准号：
7723471
负责人：
Piotr Cieplak
金额：
$ 0.58万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-07-01 至 2009-06-30
项目状态：
已结题

项目摘要

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We use the Computer Graphics Laboratory facilities to display and analyze molecular dynamics simulation results. Our research projects focus on a) refining, testing and developing the new generation of additive and nonadditive force field parameters; and b) macromolecular simulation using molecular dynamics. The work is being carried out to further develop the additive and nonadditive AMBER force field. The nonadditive AMBER parametrization includes nonadditive effects, based on atomic polarizabilities, and lone pairs interactions. A new approach to treat intra-molecular polarization has been proposed during charge development for nonadditive simulations. More thorough tests have been performed on DNA and small proteins using nonadditive force field with additional off-center (lone pairs) points located on electron-donating atoms. Additionally more tests have been performed on small protein such as ubiquitin, and short polyalanine peptides. Recently, molecular dynamics simulations have been performed in order to determine stability (free energies) and conformational transitions in short RNA loops: UUCG and UUUU.

该子项目是利用该技术的众多研究子项目之一资源由 NIH/NCRR 资助的中心拨款提供。子项目和研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金，因此可以在其他 CRISP 条目中表示。列出的机构是中心，不一定是研究者的机构。我们使用计算机图形实验室设施来显示和分析分子动力学模拟结果。我们的研究项目侧重于 a) 精炼、测试和开发新一代加性和非加性力场参数； b) 使用分子动力学进行大分子模拟。目前正在进行的工作是进一步开发加性和非加性 AMBER 力场。非加性 AMBER 参数化包括基于原子极化率和孤对相互作用的非加性效应。在非加性模拟的电荷开发过程中，提出了一种处理分子内极化的新方法。使用非加性力场对 DNA 和小蛋白质进行了更彻底的测试，并在供电子原子上设置了额外的偏心（孤对）点。此外，还对泛素和短聚丙氨酸肽等小蛋白质进行了更多测试。最近，进行了分子动力学模拟以确定短 RNA 环（UUCG 和 UUUU）的稳定性（自由能）和构象转变。