AmberMDrun: A Scripting Tool for Running Amber MD in an Easy Way

Abstract

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.

Keywords

• scripting tool
• automatically running Amber MD
• Amber MD inputs
• NVT and NPT balancing
• ten step simulation preparation
• MM-PB(GB)SA