Membrane Builder Tutorial

Objective and Overview

The objective of this tutorial is to introduce users to step-by-step procedure to build a membrane  system with CHARMM. In this tutorial we will:

  • Generate the WALP16 peptide
  • Solvate the peptide with TIP3 water and DMPC lipids
  • Minimize and equilibrate the system
Due to the complexity of lipid molecules, relatively long equilibration is required after assembly of membrane protein/peptide, lipid molecules, and water (sometimes ions).

It should be stressed here that the procedure below is not the only way to build a membrane system.

A molecular graphical view of the WALP16 peptide embedded in a DMPC membrane in an aqueous solution.

Step-by-Step for building a membrane system

pept.inp This is a step for preparing and orienting the membrane protein/peptide of your interest. In this example, a helical conformation of the transmembrane WALP16 peptide is generated using its sequence information (GWWLA LALAL ALAWW A). The helical principal axis is oriented along Z.

step1.inp To determine the system size or number of lipid molecules, one has to calculate the cross-sectional area of the protein/peptide along Z. In this example, if you plot "step1.plo", the result of the input file, you will see

Note that the asymmetry in the profile results from Leu-Ala alternation in the sequence. For the present illustration, we will simply take the average of upper and lower minima and save it in a file called "step1.str" for the next step.

step2.inp This step is to build optimal positions of pseudo-lipid big spheres, which will be used later to place real lipid molecules. In this step, we have to determine the size of the system along XY directions.

60.7 A**2 / DMPC at 303 K
64.0 A**2 / DPPC at 323 K

In this example, we will use 16 DMPC lipids for each leaflet (upper and lower to form a bilayer). Therefore, the system size can be determined from the area of both lipids and the WALP peptide. In the input,

calc BoxsizeXY = sqrt ( @Nlipid / 2.0 * 60.7 + @PeptArea )

At the end of the calculation, "step2_img.pdb" will look like these;


Note that the magenta spheres are in the primary system and the rest is in images along XY.

step3.inp We now can put lipid molecules to each position of the big sphere by randomly picking a lipid conformation from a library of DMPC. Note that the DMPC lipids in the library contain some water molecules around the head group. One may see quite some of overlaps between lipid molecules due to the random picking.

step4.inp Now, it is time to add some water molecules to fully solvate the system. Here, we will use a water box with a length of 22 A. One should determine an appropriate size based on the protein size. By starting the box from +/- 12 A along Z, we have a system size of 68 A along Z;

calc BoxsizeZ = ( 12.0 + @waterlength ) * 2.0
Once we remove all the water molecules close to the previous components (peptide, lipids, and solvation water) within 2.6, we separate water and lipids into different files ("step4_dmpc.crd" and "step4_tip3.crd").

step5.inp So far we just built the system by putting the components piece by piece, and thus each component is totally uncorrelated. After assembly in this step, we will  minimize and equilibrate the system in NVT ensemble with restraint potentials (restraint.str) to place things where they supposed to be initially.

equi1.inp We continue and continue the system equilibration in CTPA ensemble with PME (Particle Mesh Ewald) by reducing the restraint force constants. And, eventually we just let system go for free simulations.

written by Wonpil Im