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本文对人类免疫缺陷病毒(HIV-1)蛋白酶-抑制剂复合物分别在AMBER力场及极化专一性蛋白电荷(PPC)下进行了10ns的分子动力学模拟(MD),并用MM/PBSA方法计算了结合自由能。PPC是基于线性标度的量子力学计算得到的静电势拟合出的蛋白质电荷,能够更准确的描述蛋白质所处的静电环境。计算结果表明,PPC电荷计算得到的结合自由能比AMBER力场计算得到的结合自由能更接近实验值。
In this paper, the molecular dynamics simulations (MD) of human immunodeficiency virus (HIV-1) protease-inhibitor complex under AMBER force field and PPC (polar specific protein charge) The method calculates the bound free energy. PPC is based on a linear scale quantum mechanics calculated electrostatic potential to fit the protein charge, to more accurately describe the electrostatic environment in which the protein. The calculated results show that the free energy of binding calculated by PPC charge is closer to the experimental value than that calculated by AMBER force field.