College of Physics, Qingdao University, Qingdao 266071, China.
Biomolecules. 2023 Mar 31;13(4):635. doi: 10.3390/biom13040635.
MD simulations have been widely applied and become a powerful tool in the field of biomacromolecule simulations and computer-aided drug design, etc., which can estimate binding free energy between receptor and ligand. However, the inputs and force field preparation for performing Amber MD is somewhat complicated, and challenging for beginners. To address this issue, we have developed a script for automatically preparing Amber MD input files, balancing the system, performing Amber MD for production, and predicting receptor-ligand binding free energy. This script is open-source, extensible and can support customization. The core code is written in C++ and has a Python interface, providing both efficient performance and convenience.
分子动力学模拟已被广泛应用，并成为生物大分子模拟和计算机辅助药物设计等领域的有力工具，可用于估算受体和配体之间的结合自由能。然而，执行 Amber MD 的输入和力场准备工作有些复杂，对初学者来说具有一定挑战性。为了解决这个问题，我们开发了一个脚本，可以自动准备 Amber MD 的输入文件，平衡系统，进行 Amber MD 的生产模拟，并预测受体-配体的结合自由能。该脚本是开源的、可扩展的，并支持定制。核心代码是用 C++编写的，有一个 Python 接口，提供了高效的性能和便利性。
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