Bioinformatics Research Group @ TMU


Membrane Builder (version 1 )

New Version of MemBuilder is now available here.

Bioinformatics Research Group @ TMU


Challenge for the construction of the initial lipid bilayer is the main problem in setting up a simulation for membrane proteins considering protein dynamics, folding, and the mechanism of action. Almost all membrane models used in molecular dynamics simulations are usually composed of only one type of phospholipids molecule that is quite far from the native biological state, because biological membranes contain various types of lipids. Moreover, the asymmetry of lipid composition of the lipid bilayer is functionally important.

MemBuilder server prepares the initial configuration of a membrane model composed of different phospholipid molecules. This server is also dedicated to determine the lipid composition of each monolayer to support the asymmetry of the membrane bilayer.

Number of lipids in each monolayer X

Number of lipids in membrane bilayer


Thickness of membrane  (Å) 51
Length of the membrane  (Å) 56
Width of the membrane  (Å) 56 Membrane Name:
Force Field X Your email:
Neutralization:   Add concentration (M) of

   Run Minimization




Outer Layer Number of Lipids 0
% %100

Inner Layer



Number of Lipids 0



  • M. M. Ghahremanpour, S. S. Arab, S. Biook Aghazadeh, J. Zhang and D. van der Spoel (2013) MemBuilder: A Web-Based Graphical Interface to Build Heterogeneously Mixed Membrane Bilayers for the GROMACS Biomolecular Simulation Program. Bioinformatics, [First published online: November 22, 2013] doi: 10.1093/bioinformatics/btt680



Cholesterol is built using HyperChem and optimized using quantum calculations with Gaussian 03 at the Hartree-Fock level employing the 6-311G* basis set. Cholesterol topology file is built using PRODRG web server. 


Topology files for DOPC, DPPC, POPC, POPE are obtained from Biocomputing at the Calgary University. These topology files need lipid.itp file.


Topology files for DMTAP and POPG is obtained from Prof. Mikko Karttunen's group (SoftSimu). His current address is Department of Chemistry, University of waterloo.


Bioinformatics Research Group
Faculty of Biological Sciences
Tarbiat Modares University

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Contact S. Shahriar Arab: