DEVELOPMENT AND APPLICATION OF A NEW QM/MM METHOD

新QM/MM方法的开发和应用

• 批准号: 2637506
• 负责人: TAI-SUNG LEE
• 金额: $ 2.62万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-09-14 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/2637506
• 关键词: DNA methylation; method development; methyltransferase; molecular dynamics; quantum chemistry

A new combined quantum mechanical (QM) and molecular mechanical (MM) technique is proposed. The method has an intuitive approach to partition total energy into QM and MM contributions. The number of electrons of QM region is controlled by a variable chemical potential and the requirement of a well-defined closed-shell QM region is no longer needed. The contribution of QM region is enhanced by a buffer region approach this approach circumvents the boundary problem in conventional combined QM/MM methods and the accuracy of QM results should be enhanced. This method is also proposed to apply to DNA molecular systems. We will focus on the effect of the methylation of DNA molecules. The application includes the calculations on structures and energies, and the simulation of the methylation process of DNA (Cytosine-5-)-methyltransferase. We hope this work will provide an accurate and efficient approach for biomolecular system.

一种新的量子力学和分子力学相结合的方法 技术提出。该方法具有直观的分区方法 总能量转化为QM和MM贡献。量子力学的电子数 区域由可变化学势控制，并且要求 不再需要一个定义良好的闭壳层QM区域。的 QM区域的贡献通过缓冲区域方法增强， 该方法避免了传统的QM/MM组合方法中的边界问题 方法和质量管理结果的准确性有待提高。该方法 也提出适用于DNA分子系统。重点抓好 DNA分子甲基化的影响。该应用程序包括 结构和能量的计算，以及模拟 DNA（胞嘧啶-5-）-甲基转移酶的甲基化过程。我们希望这 这项工作将为生物分子生物学研究提供一种准确、有效的方法。 系统