A Shortcut to Building Lipid Bilayers Around Proteins in SAMSON

When preparing membrane protein systems for simulation, one of the most repetitive and time-consuming tasks is building a lipid bilayer around your protein. From aligning the protein to carefully setting up two asymmetric lipid layers, molecular modelers often rely on scripts or external tools—sometimes needing manual tweaking after each step.

SAMSON‘s Molecular Box Builder simplifies this process with an intuitive interface that allows you to assemble a lipid bilayer around a protein in just a few steps.

Aligning the Protein

For accurate bilayer construction, it’s important to orient the protein so that its transmembrane region aligns with the membrane plane. In SAMSON:

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

Align protein

Setting the Lipid

Next, you import and select a lipid molecule (like POPC), and set it in the Molecular Box Builder:

  1. Import the lipid into your project.
  2. Select it in the viewport or document.
  3. In the app, click Set.
  4. Choose to align it along the +Z axis to orient it correctly for the upper layer.

Align a molecule with Z-axis

Defining the Box

Now define a molecular box centered around the protein, sized appropriately to accommodate a single lipid layer. You should:

  • Enable the Center option to position the box around the origin (where we’ve centered the protein).
  • Ensure the box is just tall enough to fit one lipid.
  • Adjust spacing between lipids using the margin setting, if needed.

A box with a protein

Generating the First Lipid Layer

Be sure to enable Consider existing molecules in the box so that lipids are placed only where there’s space (i.e., avoiding the protein). Then, click Generate.

A lipid layer with a protein

Completing the Bilayer

To generate the second lipid layer:

  1. Shift the box slightly along the Z-axis so the second layer is placed under the protein.
  2. Change the lipid orientation to -Z.
  3. Click Generate again.

And there you have it: a full bilayer constructed in minutes—without writing a single line of code. ⚛️

This streamlined approach lowers the barrier to setting up complex systems for simulation and gives modelers more control through a visual, interactive environment. Whether you’re preparing a quick test system or building a physiological membrane environment, SAMSON’s Molecular Box Builder can be a strong addition to your workflow.

To learn more, consult the full guide here: Molecular Box Builder Documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at samson-connect.net.

Comments are closed.