Preparing a molecular system for simulation often involves fine-tuning and ensuring only relevant components are included. For molecular modelers, one recurring pain is determining which water molecules to keep in their simulation, especially when faced with tightly bound crystal waters around functional active sites. Improper removal can lead to inaccurate simulation results, while leaving unnecessary waters can clutter the system. In this guide, we’ll discuss how to efficiently delete existing crystal waters outside of the active site using SAMSON’s GROMACS Wizard.
Why Remove Unnecessary Water Molecules?
Crystal structures often include water molecules from crystallization that are not functional in simulations. However, not all waters are dispensable. Some tightly bound waters play a structural or functional role, particularly in active sites. Removing unnecessary water can simplify your model and increase computational efficiency without affecting the simulation’s accuracy.
Step-by-Step: Removing Crystal Waters Outside the Active Site
In SAMSON, you can selectively remove water outside the active site while preserving functional water molecules. Follow these steps:
- Select the Active Site: Identify the active site by selecting structures (e.g., ligands, water), residues, or atoms in it.
- Expand the Selection: Right-click on the current selection in the Document view or the Viewport. From the context menu, go to Expand selection > Advanced.
- Specify Water Molecules for Deletion:
In the pop-up dialog box:
- Select Water as the Node type.
- Set a distance criterion (e.g., beyond 5 Å outside of the active site).
- Enable auto-update to preview and adjust the selection.
When satisfied, click OK to confirm the selection.
- Erase the Selection: Right-click on the selection in the Document view or Viewport and click Erase selection. Only the unwanted water molecules will be removed.
By leveraging SAMSON’s capabilities, you can ensure a precise and clean selection process for your simulation needs.
When Shouldn’t You Remove Water?
While cleaning up non-functional water is generally beneficial, be cautious not to remove tightly bound waters that play active roles. For example:
- Water molecules acting as structural bridges.
- Waters that participate in catalytic reactions or ligand binding.
Always verify your selection before erasing.
Learn More
To explore this topic further, refer to the official documentation page for SAMSON’s GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.