Removing water molecules is a common part of preparing a protein structure for simulation—but removing every water can be too blunt. Some crystal waters may be tightly bound or play a functional role near a ligand or active site. Delete those by accident, and you may lose structural context you intended to preserve.
A safer approach is to make the cleanup decision locally: identify the region you want to keep, select waters beyond a chosen distance from it, inspect the result, and only then erase those waters. This lets you remove waters away from the active site while retaining nearby ones for further consideration.
Start with a deliberate reference selection
Load your structure in SAMSON, then select something that defines the region of interest—for example, a ligand, a residue, or atoms in the active site. The selection becomes the reference for expanding the selection, so check that it represents the region you actually want to preserve before continuing.
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 reference selection. The tutorial illustration shows a selection of water beyond 5 Å; treat that as an example, not a universal cutoff. The appropriate distance depends on the system and on which waters you need to keep.
If available, turn on auto-update to preview the selection as you adjust the distance. Before erasing anything, inspect the highlighted waters in the viewport or Document view. This review step is important: the selection should contain the waters you intend to remove, not waters you want to retain.
Erase only after checking
Once you have verified the selection, right-click it and choose Erase selection. If the result is not what you expected, revise the selection rather than proceeding with a broad water-removal command. A useful habit is to pause at this point and confirm that key waters near a ligand or active site remain in the structure.
This selective method is especially useful when a system contains both ordinary solvent waters and waters that may be important to the model. It does not determine which waters are biologically functional; that judgment still depends on your system and modeling goals. The selection tool simply gives you a controlled way to remove waters based on their distance from a region you specify.
Clean up the rest of the structure carefully
Water removal is only one part of pre-processing. Before the GROMACS preparation workflow, the tutorial also recommends removing alternate locations, unnecessary small molecules, and monatomic ions. Be cautious with ligands, cofactors, or other molecules you intend to simulate: do not remove them during cleanup. If you plan to keep an arbitrary molecule, you may need a topology file for it, which can be supplied during the later preparation step.
For a first pass, the 1AKI structure is used in the tutorial. In SAMSON, load it through Home > Fetch by entering 1AKI in the PDB or PDB (mmCIF) field. The preparation dialog provides the general cleanup options, but selective water deletion is preferable when you need to preserve waters in a particular region.
The main takeaway: don’t treat every water molecule as disposable by default. Define what you want to preserve, select waters outside that region, and verify the selection before deleting. For the full workflow and additional cautions, read the original pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.