Building lipid layers around membrane proteins is a common challenge for molecular modelers. Whether you’re preparing a membrane system for MD simulations or simply studying membrane-protein interactions, manually assembling lipid bilayers can be time-consuming and error-prone.
The Molecular Box Builder extension for SAMSON offers a guided way to generate layers of lipids around proteins efficiently. It helps remove the burden of trial-and-error placement, letting you focus more on the simulation science and less on system preparation logistics.
Why do lipid layers matter?
Membrane proteins function within lipid bilayers, and reproducing that environment is crucial for realistic simulations. Auto-building layers of lipids—aligned and spaced correctly—ensures spatial consistency and reduces unwanted steric clashes.
How to build a lipid monolayer around a protein
Here is an overview of how to create a single lipid layer around a membrane protein using Molecular Box Builder:
Step 1: Align the protein
This step ensures that the membrane plane aligns with a coordinate axis, typically the XY plane (with the protein oriented along the Z-axis).
- Right-click the protein in the Document view.
- Choose Move selection > Align with Z axis.
- Then choose Move selection > Center on the origin.
Step 2: Set the lipid molecule
- Import a lipid (e.g., POPC).
- Select it from the Viewport or Document view and click Set in Molecular Box Builder.
- Use the orientation option to align along
+Z, so lipid tails point along the Z-axis.
Step 3: Define the box
Create a box large enough to encompass the protein and leave space for a lipid layer on one side (e.g., the top half-space). The box center should match the protein’s center.
- Enable the Center checkbox and align with origin or specific position.
- Specify the box size and margin between lipids.
Step 4: Generate
- Activate the Consider existing molecules in the box option. This prevents lipid insertion where the protein already occupies space.
- Click Generate.
The result: a filled layer of lipids around the protein without clash or overlap.
Bonus: Lipid Bilayers
If you want a bilayer rather than a monolayer:
- Add the first lipid layer with alignment along
+Z. - Shift the box center along the Z axis.
- Add another layer with alignment along
-Z.
By stacking two layers with opposing orientations, you form a complete bilayer.
Wrapping up
The Molecular Box Builder extension streamlines the process of creating lipid environments for membrane proteins. It might not replace careful system preparation in every case, but it eliminates much of the tedium and guesswork when assembling layers. With orientation controls, margin settings, and collision avoidance, it’s easy to prototype systems quickly.
Learn more in the full documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.