Cleaning a protein structure before simulation can feel like a simple housekeeping task: remove water, discard small molecules, and move on. But a blanket cleanup can remove water molecules that matter. Some crystal waters are tightly bound or participate in an active site, so deleting every water may remove part of the environment you intended to model.
The challenge is to remove unnecessary waters without losing those near a functional region. In SAMSON’s GROMACS Wizard, you can select waters by their distance from a region you want to preserve, inspect the selection, and erase only the waters outside it.
Start with the region you want to keep
First, select the structures, residues, or atoms that define the active site or other region of interest. This might include a ligand, nearby residues, or particular atoms. The selection acts as the reference for finding waters around that region.
Right-click the selection in the Document view or the Viewport, then choose Expand selection > Advanced. In the dialog, set the node type to Water and choose beyond a distance from the current selection. This selects waters outside the chosen distance, rather than waters close to the active site.
The documentation illustrates this with a 5 Å example. Treat that as an example, not a universal cutoff: the appropriate distance depends on your system and what you need to preserve. If you are unsure, use a conservative selection and review it before deleting anything.
Inspect first, erase second
If available, enable auto-update in the selection dialog to preview which waters are selected. After confirming the selection, click OK. Then check the highlighted molecules in the viewport or Document view. Make sure the waters you want to keep are not included.
Only after verifying the selection should you right-click it and choose Erase selection. This two-part workflow—select, inspect, then erase—helps avoid turning a distance-based cleanup into an accidental removal of important molecules.
When broad water removal is appropriate
The Home > Prepare workflow also offers a Remove water option. It can be useful when removing all existing water is suitable for your system. However, it is not appropriate for every model. If the structure contains tightly bound or active-site waters that you want to retain, use a more selective approach instead of removing water indiscriminately.
As you clean the structure, consider the other contents too. Alternate locations can be removed during preprocessing. Unneeded ligands and other small molecules may also be removed, but keep any molecule you intend to simulate. Monatomic ions can be removed as part of cleanup. Adding hydrogens at this stage is optional, since GROMACS can add them later.
For arbitrary molecules that you want to keep, do not simply erase them because they are difficult to prepare. They may need topology files, such as .itp files, generated with an external tool and supplied during the later preparation step.
A practical check before continuing
- Identify the active site or other region whose nearby waters should remain.
- Select waters beyond a distance from that region using Expand selection > Advanced.
- Preview and verify the selected waters before erasing them.
- Check that ligands, cofactors, ions, and other molecules you need have not been removed.
Once the structure contains the molecules you intend to simulate, continue to the GROMACS preparation workflow. For the complete steps and additional notes, learn more in the preprocessing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.