Overview

MM/GB(P)SA free energy calculations using various programs

Skill Level: Advanced

Language: English

Workload: 2 hours total

Topic: Computational Biophysics

Overview: The course will show how to use tools for calculating binding free energy on the simulation trajectories produced by popular Molecular Dynamics Simulation engines.

Course Description: This online course aims at demonstrating how to perform MM/GB(P)SA calculations on HPC platforms. These calculations are one of the mostly performed calculations in drug discovery studies. Typically, these are used to estimate binding affinities of ligand molecules to target biomolecules (ex: receptor proteins). 

Course Contents:

Lesson1: MM/PBSA calculation using CaFE (NAMD)

Lesson2: MM/GB(P)SA Using AmberTools   (Amber)

Lesson3: MM/PBSA calculation using gmx_MMPSA (Gromacs)

Who Should Enroll: Individuals interested in performing MM/GB(P)SAcalculations on HPC platforms.

Prerequisites:

Basic knowledge in Molecular Dynamics simulations

Familiarity with Linux/Unix operating systems

Basic Knowledge in slurm job submission etc on a HPC

General knowledge in MM/GB(P)SA calculations

Tools, libraries, frameworks used: Python, VMD, NAMD, AmberTools, Gromacs

Learning Objectives: Installing popular MM/GB(P)SA tools on HPC and being able to perform these energy calculations on HPC systems

About the instructor(s): https://akademi.itu.edu.tr/tr/badays/Sefer-Baday/