Water is everywhere in biological systems, but when it comes to preparing a protein structure for simulations in GROMACS, not all water molecules need to stay. In fact, a common challenge faced by molecular modelers is identifying and removing only non-functional crystal water molecules from a system, while preserving tightly bound waters that play a role in the active site or structural integrity.
If you’ve ever loaded a PDB file and wondered how to keep only the biologically meaningful waters, you’re not alone. While it’s tempting to clear out all water molecules to start fresh, that decision can lead to unrealistic behavior if you remove essential crystallographic waters.
Fortunately, the GROMACS Wizard in SAMSON makes this task significantly easier with a targeted approach that combines selection tools and spatial criteria. Here’s how you can remove only the unnecessary water molecules from your system while staying confident you’re not deleting functionally important ones.
Step-by-Step: Select and Remove Non-Active Site Water
- Select the active region: Click on structures involved in the active site — this might include a ligand, some residues, or water molecules. This initial selection defines the spatial context for retaining useful waters.
- Expand your selection based on distance: Right-click your selection and navigate to
Expand selection > Advanced. In the pop-up dialog, choose Water as the Node type, and specify a distance (e.g., beyond 5 Å) to select only water molecules distant from the active site. You can auto-update to preview the selection before applying it. - Erase irrelevant water: With water molecules outside the active region selected, right-click again and choose Erase selection.
This approach helps preserve water molecules that are tightly bound or functionally significant, whether they stabilize the structure or are involved in catalysis.
Some Tips to Keep in Mind
- The appropriate cutoff distance (e.g., 5 Å) depends on the nature of your system — larger distances may remove more peripheral water, but exercise caution based on structural data.
- If in doubt, consult the literature or structural studies associated with your protein to identify known active-site waters.
This selective cleaning process helps you preserve realism in your simulations while ensuring the system is not cluttered with irrelevant solvent molecules. It’s especially helpful for enzyme catalysis simulations or ligand-binding studies, where certain waters play key mechanistic roles.
To learn more, see the full documentation page for pre-processing in the GROMACS Wizard:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.