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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 在其他地方详细描述了所有原子琥珀色场，并且在这里只有必要概述最强烈影响生物分子构象性质的参数。为了实现正确的动态行为（构象和寿命），二面参数是价值最重要的术语。在用琥珀色的寡糖模拟的GLYCAM参数的开发中，我们广泛使用量子计算，以得出适当的系数，扭转相移和平衡值的值。由于寡糖和蛋白质的极性，由部分原子电荷确定的静电相互作用与扭转项一样重要。这些电荷不仅要导致相对构象能的正确再现，而且还会导致生物分子与其水性环境之间的正确相互作用能。尽管部分电荷是计算静电性能的有用模型，但它们是非物理的，并且计算中使用了许多方法。在琥珀内，部分电荷是通过拟合量子机械静电电势（ESP-Charges）来确定的。鉴于我们是由我们的GlyCAM参数化产生的发展，以生成在肽上表现良好的参数集，并且与GlyCAM参数兼容，必须解决一些属性。通常，所有价项将继续从量子机械计算得出，主要是在B3LYP/6-31 ++ G **级别上进行。但是，尤其是三个领域正在重新审查1-4个缩放率，氧气对包含氧气以及1-4缩放，扭转项，静电相互作用和电荷极化之间的复杂关系。