基于蛋白质结构的准正则定域轨道(QCLO)方法研究

N. Nishino, T. Hirano, T. Nishimura, S. Koike, F. Sato
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摘要

我们开发了一个密度泛函(DF)程序,ProteinDF,用于蛋白质的全电子计算。为了克服大尺度分子收敛问题的困难,我们提出了一种新的局域轨道(LO),称为准正则轨道(QCLO)。本研究提出了以氢键和盐桥等二级结构为中心的改进收敛过程。通过与原方法的总能量、收敛历史和初始状态与收敛状态之间的Mulliken种群差值进行比较,讨论了改进过程的有效性。我们证明了新的收敛过程比以前的收敛过程给出了更好的初始猜测。该方法可用于非常大规模蛋白质的安全、自动全电子DF计算
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Study of the Quasi-Canonical Localized Orbital (QCLO) Method Based on Protein Structures
We have developed a density functional (DF) program, ProteinDF, for all-electron calculation on proteins. In order to overcome difficulties of a convergence problem in large-scale molecules, we have already proposed new localized orbital (LO), which named quasi-canonical LO (QCLO). In this study, improved convergence process which focused on the secondary structure such as hydrogen bonds and salt-bridge is proposed. The effectiveness of the improved process was discussed by comparing with the values of the original method, i.e. the total energy, convergence history and difference of Mulliken populations between initial and converged states. We proved the new convergence processes gave significantly better initial guess than previous one. This method could be useful for safe and automatic all-electron DF calculations on very large-scale proteins
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