This workshop walks through the process of perfprming a basic MM-GBSA analysis of a molecular dynamics simulation of a protein-ligand complex to estimate the ligand binding free energy. The approach here uses OpenMM with a little help from ParmEd.
This example uses data from a simulation performed using OpenMM, but could readily be adapted for use with simulations run with Amber or GROMACS (and maybe CHARMM).
The simplest way to run the workshop on your own laptop/workstation is to clone this repository and execute the supplied run_notebook.sh script.
Charlie Laughton charles.laughton@nottingham.ac.uk