Building a Lipid Membrane Around a Protein in SAMSON

Creating realistic membrane-protein systems is often a prerequisite in molecular dynamics simulations, but it can take time to carefully place lipids around a protein, avoid clashes, and ensure appropriate orientation. The Molecular Box Builder extension in SAMSON helps solve this common challenge: it allows you to generate lipid layers—single or bilayer—around proteins with just a few steps.

In this guide, we explore a practical way to build a single lipid layer around a protein using the Molecular Box Builder. This method minimizes molecule overlap, aligns lipids properly, and speeds up membrane setup.

1. Align the Protein

Start with your protein structure loaded into SAMSON. To define the right spatial frame:

  1. Right-click the protein in the Document view.
  2. Select Move selection > Align with Z axis.
  3. Then choose Move selection > Center on the origin.

Align protein

2. Set the Lipid Molecule

Load a lipid molecule of your choice (e.g., POPC). In the Molecular Box Builder app:

  1. Select the lipid from the Viewport or Document view.
  2. Click Set.
  3. Align its principal axis to +Z.

Align a molecule with Z-axis

3. Define the Box

Now define the box that will contain your lipid layer:

  1. Check Center and position the box around the protein’s center.
  2. Set the X and Y dimensions to control membrane area.
  3. Adjust the Z-thickness for a single layer.
  4. If needed, define a margin between molecules for tighter or looser packing.

A box with a protein

4. Generate the Lipid Layer

To prevent overlapping with your protein structure:

  1. Enable Consider existing molecules in the box.
  2. Click Generate to populate the box with lipids in non-overlapping positions.

And that’s it—you now have a lipid layer surrounding your protein.

A lipid layer with a protein

Optional: Build a Bilayer

For a full membrane model, you can add another leaflet:

  1. Start by creating the top layer aligned to +Z.
  2. Shift the box center downward in the Z-direction.
  3. Set lipid alignment to -Z and generate the second layer.

This results in a bilayer aligned with the protein embedded in between.

Creating lipid layers around proteins is a common molecular modeling task that can be time-consuming when done manually. With SAMSON’s Molecular Box Builder, the process becomes faster and more reliable, allowing users to focus more on simulations and less on structural setup.

To explore more features or build more complex assemblies, visit the Molecular Box Builder documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.

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