Bioinformatics Research Group @ TMU

MemBuilder Membrane Builder (version 1 )


Bioinformatics Research Group @ TMU
 

Membuilder
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MemBuilder is a web-based graphical user interface to generate homogenous and heterogenous lipid bilayers. It is implemented by using Perl and C programming languages and Java Script is also partly appplied to make web interface.

Users on MemBuilder can specify type and concentration of lipid molecules to build desired membrane. MemBuilder has eighteen different lipid molecules and support four different force fields including both all-atom and united-atom force fields that can be selected upon users' request. MemBuilder randomly place selected lipids to build the whole membrane and then performs energy minimization at the presence of water and ions to decrease local stresses inside the lipid bilayer that will take a few minutes according to the system size.

This web server help the user to generate GROMACS input files necessary to build a membrane system for molecular dynamics simulation.

Please note that

Download GROMOS43a1-S3 and Slipid/AMBER force field sources from download page and put them into the GROMACS directory = /usr/local/gromacs/share/top.

Download topology file (.itp) for each selected lipid molecule and put it in the work directory that you want to run simulation.


 

 

Bioinformatics Research Group
Faculty of Biological Sciences
Tarbiat Modares University

All rights reserved.

Contact S. Shahriar Arab:
sh.arab@modares.ac.ir