Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
J Chem Theory Comput. 2022 May 10;18(5):3089-3098. doi: 10.1021/acs.jctc.2c00113. Epub 2022 Apr 6.
Here, we present a new analysis program, AIM, that allows extracting the vibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infrared spectroscopy modeling. The constructed Hamiltonians can be used as input for spectral calculations allowing the calculation of infrared absorption spectra, vibrational circular dichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of the structure and dynamics of proteins. We will explain the essence of how AIM works and give examples of the information and spectra that can be obtained with the program using the Trypsin Inhibitor as an example. AIM is freely available from GitHub, and the package contains a demonstration allowing easy introduction to the use of the program.
在这里，我们提出了一个新的分析程序 AIM，该程序允许使用分子动力学轨迹提取振动酰胺 I 哈密顿量，用于蛋白质红外光谱建模。构建的哈密顿量可作为光谱计算的输入，允许计算红外吸收光谱、振动圆二色性和二维红外光谱。这些光谱学允许研究蛋白质的结构和动力学。我们将解释 AIM 工作的本质，并使用胰蛋白酶抑制剂作为示例，给出可以使用该程序获得的信息和光谱的示例。AIM 可从 GitHub 上免费获得，该软件包包含一个演示，允许轻松引入程序的使用。
