GROMACS Tutorial

Protein-Ligand Complex

Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore


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. If this is not the case, please refer to basic tutorial material before attempting this one.

This tutorial assumes you are using a GROMACS version in the 5.x series.

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Looking for the old version? Click here. Please note that the old version will be removed in the near future.

These tutorials were originally written while I was a member of Dr. David Bevan's research group at Virginia Tech.

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