This example will guide a new user through the process of setting up a simulation system containing a protein (T4 lysozyme L99A/M102Q) in complex with a ligand. This tutorial focuses specifically on issues related to dealing with the ligand, assuming that the user is familiar with basic GROMACS operations and the contents of a topology. If this is not the case, please refer to a more basic tutorial before attempting this one.

This tutorial requires a GROMACS version in the 2025.x series.

Looking for the older (2018) version of this tutorial? You can find it here.