EP 10 | Protein-Ligand MD Simulation in Gromacs-A to Z | all reusable commands and files provided

Introduction

This tutorial will guide you through the process of performing Molecular Dynamics (MD) simulations using Gromacs, specifically focusing on a protein-ligand complex. By following this step-by-step guide, you can replicate the simulation for any protein-ligand pair with universal commands provided.

Step 1: Prepare Your Files

Before starting the simulation, ensure you have the necessary files:

• Docked complex file (from previous docking simulations, e.g., UCSF Chimera).
• Gromacs codes and files available on GitHub.

Actions:

• Download and extract the files from the GitHub repository.
• Ensure the complex file is in a suitable format, such as PDB.

Step 2: Create Topologies for Protein and Ligand

You need to split the complex file into two parts: one for the receptor (protein) and one for the ligand.

Actions:

1. Open the complex file in UCSF Chimera.
2. Delete the protein chain to isolate the ligand.
3. Add hydrogens to the ligand:
   • Go to Tools > Structure Editing > Add Hydrogens.
4. Save the ligand as a .mol2 file, naming it LIG.
5. Repeat the process to isolate the receptor, save it as a .pdb file, naming it REC.

Step 3: Modify the Ligand File

You need to make specific edits to the ligand's .mol2 file for compatibility with Gromacs.

Actions:

1. Open the LIG.mol2 file in a text editor.
2. Ensure the first line reads @TRIPOS MOLECULE.
3. Change any reference to the original file's name to LIG.
4. Save and close the file.

Step 4: Generate Topologies Using SwissParam

Generate the necessary topology files for the ligand using the SwissParam server.

Actions:

1. Go to the SwissParam website.
2. Upload the LIG.mol2 file.
3. Download the resulting ZIP file containing the topology files.
4. Extract and place these files in your working directory.

Step 5: Prepare Gromacs Commands

With the topology files ready, you can now proceed to set up your Gromacs simulation.

Actions:

1. Open a terminal in your working directory.
2. Load Gromacs (if necessary) with the command:

   source /path/to/gromacs/bin/GMXRC
   

3. Run the following command to prepare the protein topology:

   gmx pdb2gmx -f REC.pdb -o REC_processed.gro -water spce
   

   • Select the appropriate force field and water model when prompted.

Step 6: Create a Simulation Box

Define the simulation space around your protein-ligand complex.

Actions:

1. Use the command:

   gmx editconf -f REC_processed.gro -o REC_box.gro -c -d 1.0 -bt cubic
   

2. Solvate the system:

   gmx solvate -cp REC_box.gro -cs spc216.gro -o REC_solv.gro
   

Step 7: Add Ions

Neutralize the system by adding ions.

Actions:

1. Prepare the ions file:

   gmx grompp -f ions.mdp -c REC_solv.gro -p topol.top -o ions.tpr
   

2. Generate ions:

   gmx genion -s ions.tpr -o REC_solv_ions.gro -p topol.top -neutral
   

Step 8: Energy Minimization

Minimize the energy of the system before proceeding to MD simulations.

Actions:

1. Prepare the energy minimization:

   gmx grompp -f em.mdp -c REC_solv_ions.gro -p topol.top -o em.tpr
   

2. Run energy minimization:

   gmx mdrun -deffnm em
   

Step 9: Equilibration

Perform equilibration of the system using NVT and NPT ensembles.

Actions:

1. Prepare NVT equilibration:

   gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
   

2. Run NVT equilibration:

   gmx mdrun -deffnm nvt
   

3. Prepare NPT equilibration:

   gmx grompp -f npt.mdp -c nvt.gro -p topol.top -o npt.tpr
   

4. Run NPT equilibration:

   gmx mdrun -deffnm npt
   

Step 10: Production MD Run

Finally, execute the MD simulation.

Actions:

1. Prepare the MD run:

   gmx grompp -f md.mdp -c npt.gro -p topol.top -o md.tpr
   

2. Run the MD simulation:

   gmx mdrun -deffnm md
   

Conclusion

You have successfully set up and executed an MD simulation using Gromacs for a protein-ligand complex. Key steps included preparing and modifying topology files, setting up the simulation box, adding solvent and ions, and performing equilibration followed by the MD run. Next, consider visualizing the output trajectories and analyzing the results for further insights into the molecular dynamics of your complex.