Development and testing of a general amber force field
Development and testing of a general amber force field
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DOI：
10.1002/jcc.20035
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发表时间：
2004-07-15
影响因子：
3
通讯作者：
Case, DA
中科院分区：
文献类型：
--
作者：
Wang, JM;Wolf, RM;Case, DA
本文描述了有机分子的一般琥珀力场（GAFF）。GAFF被设计为与现有的蛋白质和核酸的琥珀力场兼容，并且具有由H，C，N，O，S，P和卤素组成的大多数有机和药物分子的参数。它使用一个简单的函数形式和有限数量的原子类型，但结合了经验和启发式模型来估计力常数和部分原子电荷。GAFF在测试用例中的表现令人鼓舞。在测试I中，将74个晶体学结构与GAFF最小化结构进行比较，其中均方根位移为0.26埃，这与Tripos 5.2力场的均方根位移（0.25埃）相当，并且优于MMFF 94和CHARMm的均方根位移（分别为0.47和0.44埃）。在测试II中，对22个核酸碱基对进行气相最小化，并将最小化的结构和分子间能量与MP2/6 - 31G * 结果进行比较。位移和相对能量的均方根分别为0.25和1.2千卡/摩尔。这些数据与Parm99/RESP的结果（0.16埃和1.18 kcal/mol）相当。分别），其被参数化为这些碱基对。测试III研究了用于Parm99力场开发的71种构象对的相对能量。相对能量的RMS误差（与实验相比）约为0.5 kcal/mol。GAFF可以以自动方式应用于广泛的分子。使其适用于合理的药物设计和数据库检索。(C)2004 Wiley Periodicals，Inc.
We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Angstrom, which is comparable to that of the Tripos 5.2 force field (0.25 Angstrom) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Angstrom, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 Angstrom and 1.18 kcal/mol. respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion. making it suitable for rational drug design and database searching. (C) 2004 Wiley Periodicals, Inc.