DEVELOPMENT & INCORPORATION OF CARBOHYDRATE FORCE FIELDS FOR USE WITH AMBER

发展

• 批准号: 8361788
• 负责人: ROBERT J WOODS
• 金额: $ 7.09万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-02-01 至 2012-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8361788
• 关键词: Address; Amber; Area; Behavior; Carbohydrates; Charge; Complex; Development; Electrostatics; Environment; Equilibrium; Funding; Grant; Light; Mechanics; Methods; Modeling; Molecular Conformation; National Center for Research Resources; Nature; Oligosaccharides; Oxygen; Peptides; Phase; Principal Investigator; Property; Proteins; Relative (related person); Reproduction; Research; Research Infrastructure; Resources; Source; Torsion; United States National Institutes of Health; aqueous; cost; quantum; simulation

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The all atom AMBER force field has been described in detail elsewhere, and it is only necessary here to outline the parameters that most strongly influence the conformational properties of biomolecules. To achieve correct dynamic behavior (conformations and lifetimes), the dihedral parameters are the most important of the valence terms. In the development of the GLYCAM parameters for oligosaccharide simulations with AMBER, we made extensive use of quantum calculations to derive appropriate values for the coefficients, torsional phase shifts, and equilibrium values. Due to the polar nature of oligosaccharides and proteins, electrostatic interactions, determined by partial atomic charges, are as important as the torsion terms. It is essential that these charges result not only in a correct reproduction of relative conformational energies, but also in the correct interaction energies between the biomolecule and its aqueous environment. Although partial charges are a useful model for computing electrostatic properties, they are non-physical and there have been numerous methods employed in their calculation. Within AMBER the partial charges are determined by fitting to quantum mechanical electrostatic potentials (ESP-charges). In light of the developments arising from our parameterization of GLYCAM, to generate a parameter set that performs well on peptides, and that is compatible with the GLYCAM parameters, several properties will have to be addressed. In general, all of the valence terms will continue to be derived from quantum mechanical calculations, mostly performed at the B3LYP/6-31++G** level. But three areas in particular are being reexamined, namely, the use of 1-4 scaling, the inclusion of lone pairs on oxygen, and the complex relationship between 1-4 scaling, torsion terms, electrostatic interactions and charge polarization.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 子项目的主要研究者可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 全原子琥珀力场已经在其他地方详细描述过了，这里只需要概述最强烈影响生物分子构象特性的参数。为了获得正确的动力学行为（构象和寿命），二面角参数是最重要的价项。在开发的GLYCAM参数与琥珀寡糖模拟，我们广泛使用量子计算，以获得适当的值的系数，扭转相移，和平衡值。由于寡糖和蛋白质的极性性质，由部分原子电荷决定的静电相互作用与扭转项一样重要。重要的是，这些电荷不仅导致相对构象能的正确再现，而且导致生物分子与其水性环境之间的正确相互作用能。虽然部分电荷是计算静电性质的有用模型，但它们是非物理的，并且在其计算中采用了许多方法。在AMBER中，部分电荷通过拟合量子力学静电势（ESP-电荷）来确定。根据我们的GLYCAM参数化所产生的发展，为了生成对肽表现良好并且与GLYCAM参数兼容的参数集，必须解决几个特性。一般来说，所有的价项将继续从量子力学计算中推导出来，主要在B3 LYP/6-31++G** 水平上进行。但是，特别是三个领域正在重新审查，即1-4标度的使用，包括孤对氧，1-4标度，扭转项，静电相互作用和电荷极化之间的复杂关系。