Water molecules in protein structures from the Protein Data Bank (PDB) can either be essential for function or relics from crystallographic data that don’t matter for your simulation. Knowing how to selectively remove undesired water molecules while preserving those in or near the active site is crucial for setting up accurate molecular dynamics (MD) simulations.
In GROMACS simulations, it’s common practice to remove existing solvent so that it can be replaced with a freshly added solvent box and ions. However, if you indiscriminately delete all water molecules, you risk removing important ones that stabilize the protein-ligand complex or are involved in catalytic activity.
Fortunately, with the GROMACS Wizard in SAMSON, you can make careful selections and preserve functionally important waters. Here’s a step-by-step guide on how to do exactly that.
Identifying Functional Waters
Before deleting waters, ask yourself:
- Is the water hydrogen-bonded to a ligand, metal, or residue in the active site?
- Does literature or experimental data suggest a role for specific waters?
If so, these are likely worth keeping.
Selecting and Deleting Crystal Waters Outside of the Active Site
To remove only the unnecessary solvent and preserve important waters, follow these steps:
1. Select Key Atoms or Residues in the Active Site
Use the selection tools in Document view or Viewport to manually pick atoms or residues in the region of interest.
2. Expand Selection to Find Neighboring Water
Right-click your current selection and go to Expand selection > Advanced.
In the pop-up window, specify:
- Node type: Water
- Relation: beyond
- Distance: e.g., 5 Å
Click auto-update to see which water molecules fall beyond the specified distance. Adjust as needed.
3. Delete the Selected Waters
Once the far-field waters are selected and verified, right-click in the Document view and choose Erase selection.
This preserves the waters close to your active site—a small step that can help maintain biological relevance in your MD simulations.
Why This Matters
Water molecules are often more than just structural noise. Tightly bound waters can act as proton donors or acceptors, bridge substrates and active site residues, or maintain critical protein conformations.
By taking a few extra steps during preprocessing, you ensure better data quality and avoid artifacts that stem from overzealous solvent removal. This method gives you precise control over the environment you want to simulate, which is especially important when simulating enzymatic reactions or ligand binding.
To learn more about this and other preprocessing strategies, visit the full documentation here:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.