MAB, A GENERALLY APPLICABLE MOLECULAR-FORCE FIELD FOR STRUCTURE MODELING IN MEDICINAL CHEMISTRY
MAB, A GENERALLY APPLICABLE MOLECULAR-FORCE FIELD FOR STRUCTURE MODELING IN MEDICINAL CHEMISTRY
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DOI：
10.1007/bf00124456
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发表时间：
1995-06-01
影响因子：
3.5
通讯作者：
MULLER, K
中科院分区：
文献类型：
--
作者：
GERBER, PR;MULLER, K
给出了一种新的、普遍适用的分子力场的数学公式、参数化方案和结构结果。其主要特点是参数自动分配方案，一致的联合原子近似，不存在元素以外的原子类型，用几何氢键项取代静电项，不需要部分原子电荷分配，以及严格遵守有限范围设计。由于省略了所有氢原子，通过适当的网络分析动态地计算了最佳氢键模式。对于从剑桥结构数据库中选择的1589个结构的测试集，仅基于给定的元素列表和高结构精化标准，根据结构的大小和灵活性，协议平均为键为2 PM，价角为2度，原子位置的均方根偏差为10到20 PM。对蛋白质和DNA低聚体的大规模力场结构特性的更多定性测试显示出令人满意的性能。
The mathematical formulation, parametrization scheme, and structural results of a new, generally applicable molecular force field are presented. The central features are a scheme for automatic parameter assignments, the consistent united-atom approximation, the absence of atom types other than elements, the replacement of electrostatic terms by geometrical hydrogen-bonding terms, the concomitant lack of a need for partial atomic charge assignment and the strict adherence to a finite-range design. As a consequence of omitting all hydrogen atoms, optimal hydrogen-bond patterns are computed dynamically by appropriate network analyses. For a test set of 1589 structures, selected from the Cambridge Structural Database solely on the grounds of a given element list and criteria for high structure refinement, the agreements are on average 2 pm for bonds, 2 degrees for valence angles and 10 to 20 pm for the root-mean-square deviation of atom positions, depending somewhat on size and flexibility of the structures. More qualitative testing of large-scale structural properties of the force field on proteins and DNA oligomers revealed satisfactory performance.