Cleaning up a molecular system before running simulations is a critical step for ensuring reliable results. One common issue for molecular modelers involves deciding what to do with the crystal waters found in protein structures. While some waters are essential for maintaining active site function, others can be safely removed to streamline your simulations. But how do you make that distinction effectively?
In this blog post, we’ll walk you through the procedure to selectively remove crystal waters that are not part of the active site, using the GROMACS Wizard in the SAMSON platform.
The Challenge: To Keep or Remove Waters?
Molecular systems derived from databases like the Protein Data Bank often contain water molecules embedded in the crystal structure. While tightly bound waters around the active site might be critical for the system’s behavior, others outside the active site can often be safely removed to simplify simulation complexity and reduce computational cost.
Step-by-Step Guide for Selective Removal
Here’s how you can remove non-essential waters from your molecular system while keeping waters within the active site intact:
- Select the Active Site: Use the GROMACS Wizard’s tools to carefully select your active site’s relevant features. This might include the ligand, specific residues, or tightly bound water molecules.
- Expand Selection: Right-click the selection in the Document view or the Viewport and navigate to Expand selection > Advanced. In the dialog box that appears, you can refine your selection criteria. For instance, specify the “Water” node type and set a distance beyond which waters should be identified and removed.
- Preview Your Selection: Use the auto-update feature to visualize which waters have been chosen for removal. Verify that critical waters in the active site remain unselected while others are highlighted for deletion.
- Erase Unnecessary Waters: Once your selection is verified, right-click the selection again and choose Erase selection. This ensures only critical waters are retained, and the others are removed from your system.
The following image demonstrates a scenario where waters beyond a specified distance (e.g., 5 Angstroms) from the active site are identified for removal:
Why This Matters
By fine-tuning your molecular system and removing unnecessary waters outside the active site, your simulations will run more efficiently without compromising accuracy. This is a delicate but highly valuable step in molecular modeling that helps you focus computational resources on relevant interactions.
Going Further
For a more detailed walkthrough or to learn about other system preparation techniques, check out the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Start your molecular modeling journey by downloading SAMSON at samson-connect.net.