When setting up molecular simulations, one challenge frequently encountered by molecular modelers is determining how to handle crystal water molecules in a protein system. Some waters, like tightly bound or active-site waters, are functional and should be retained. Others can negatively affect your simulation and need to be removed. Managing these appropriately ensures accurate simulations while avoiding unnecessary computational expense.
The GROMACS Wizard in SAMSON provides an efficient and intuitive way to handle crystal water molecules, whether you want to remove all or selectively keep specific ones. Let’s break this down.
Removing All Crystal Waters
If your molecular design doesn’t require the presence of water molecules, simply use the Home > Prepare option to Remove water. This action will remove all water molecules from the system with ease. However, be cautious if your simulation depends on functional water molecules.
Selective Removal of Crystal Waters Outside the Active Site
For simulations that require preserving active-site waters while removing non-essential ones, SAMSON’s GROMACS Wizard offers a streamlined solution. Here’s how to achieve it:
- Select structures or residues in the active site. Start by carefully selecting the ligand, active-site water molecules, or other residues you wish to preserve. This can be done from the Document view or the Viewport.
- Expand the selection. Right-click on your selection, navigate to Expand Selection > Advanced in the context menu. This opens a pop-up dialog where you can manage your selection criteria.
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Choose crystal water to remove. Set Water as the Node type and specify a distance criterion using “beyond” the active site. Activate the auto-update option to visualize the selection boundaries, and confirm by clicking OK.
- Erase selected water molecules. Verify the final selection. Once satisfied, right-click on the selection from the Document view or Viewport, and select Erase selection.
This approach provides detailed control over your system, ensuring only relevant waters stay in the system while optimizing the computational cost of your simulations.
Final Thoughts
Effective preparation of the system is crucial for reliable molecular simulation. SAMSON’s GROMACS Wizard simplifies the process of handling water molecules, allowing molecular modelers to tailor their system to their simulation’s specific requirements. To delve into more details, visit the full documentation at GROMACS Wizard Pre-processing Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at samson-connect.net.