One of the most common tasks molecular modelers face when preparing a simulation is cleaning up PDB structures imported from the Protein Data Bank. These files often contain crystal waters—some of which are essential for maintaining protein active sites, while others are simply background hydration. Removing all water molecules indiscriminately could compromise your simulation’s biological relevance, but manually selecting waters is tedious and error-prone. If you’ve faced this dilemma, you’re not alone—and there’s a smarter way to do it.
When using the GROMACS Wizard in SAMSON, you can fine-tune water molecule deletion to preserve key waters that reside in the active site, while removing the rest. Here’s how it can be done efficiently using SAMSON’s selection tools:
Selective Water Deletion: The Smart Approach
Instead of removing all water molecules during pre-processing, follow these steps to delete only those outside of functional regions:
- Select what matters: Start by selecting key parts of your system, such as a ligand or specific residues in the active site. This selection defines the region you want to preserve.
- Expand intelligently: Right-click the selection in either the Document view or the Viewport. Choose Expand selection > Advanced in the context menu.
- Target distant waters: In the dialog, set the Node type to Water, and choose the expansion mode as beyond a certain distance threshold (e.g., 5 Å) from your selection. Enable Auto-update to preview what will be selected.
- Clean specifically: Once you’re satisfied with the selection, click OK. Then right-click again and select Erase selection. This keeps critical water molecules intact, while erasing non-essential ones.
This method allows you to merge automation with expert knowledge of your system. You protect catalytically important water molecules, maintain hydrogen bonding around the active site, and avoid manually editing large files.
Why This Matters
Removing all crystal waters might seem harmless at first, but water molecules in active sites often play roles in:
- Maintaining structural integrity
- Participating in catalytic cycles
- Stabilizing ligand binding
Preserving these functionally important interactions can be essential for ensuring your simulations yield meaningful insights. By using SAMSON’s GROMACS Wizard and its advanced selection tools, you gain precision without losing speed.
To learn more about pre-processing with the GROMACS Wizard in SAMSON, visit the official documentation page:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.