Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives
Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives
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DOI：
10.1039/b509557c
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发表时间：
2005-12-21
影响因子：
3.3
通讯作者：
Mezey, PG
中科院分区：
文献类型：
--
作者：
Exner, TE;Mezey, PG
大量的构象和化学修饰的变体的蛋白质crambin被用来广泛测试现场适应的可调密度矩阵汇编程序（FA-ADMA）的方法开发的从头计算质量的量子化学计算的蛋白质和其他大分子在早期出版物中介绍。在这种方法中，模糊密度矩阵分裂计划的原始可调密度矩阵汇编程序（ADMA）的方法已作出更有效的结合使用点电荷的方法来近似的影响，一个给定的大分子的额外的，遥远的部分，在量子化学计算的每个片段。以这种方式，较小的母体分子可以用于片段生成，同时实现在原始ADMA方法中仅用大母体分子可以获得的准确度。然而，在这两种方法中，相对于Hartree-Fock结果的误差可以通过选择足够大的母体分子而降低到任何阈值以下，这可以用新方法更有效地完成。为了获得可靠的测试结果的准确性，通过新的方法相比，传统的Hartree-Fock计算，我们进行了大量的能量计算的蛋白质crambin使用各种构象中的蛋白质数据库，各种质子化状态，和侧链突变。此外，为了测试该方法用于蛋白质-溶剂相互作用研究的性能，研究了由于与乙醇和单个和多个水分子形成复合物而引起的能量变化。
A large number of conformations and chemically modified variants of the protein crambin were used to extensively test the field-adapted adjustable density matrix assembler (FA-ADMA) method developed for ab initio quality quantum chemistry computations of proteins and other macromolecules introduced in an earlier publication. In this method, the fuzzy density matrix fragmentation scheme of the original adjustable density matrix assembler (ADMA) method has been made more efficient by combining it with an approach of using point charges to approximate the effects of additional, distant parts of a given macromolecule in the quantum chemical calculation of each fragment. In this way, smaller parent molecues can be used for fragment generation, while achieving accuracy that can be obtained only with large parent molecules in the original ADMA method. Whereas in both methods the error relative to the Hartree-Fock result can be reduced below any threshold by choosing large enough parent molecules, this can be done more efficiently with the new method. In order to obtain reliable test results for the accuracy obtainable by the new method when compared to conventional Hartree-Fock calculations, we performed a large number of energy calculations for the protein crambin using various conformations available in the Protein Data Bank, various protonation states, and side chain mutations. Additionally, in order to test the performance of the method for protein-solvent interaction studies, the energy changes due to the formation of complexes with ethanol and single and multiple water molecules were investigated.