g_membed

Introduction

We have developed a Gromacs tool, g_membed, to efficiently insert a protein into a fully hydrated and equilibrated membrane. Therefore, the protein is reduced in size in the membrane plane, overlapping molecules (lipids, waters, etc.) are removed and finally a short molecular dynamics run (typically 1,000 steps) is performed to grow the protein slowly to its full size.


Fig 1: Graphical impression of the embedding process (Reaction Center in a DOPC bilayer).

Also in highly curved bilayers, proteins can be inserted efficiently, as illustrated by the vesicle system.
Fig 2: Beta Barrel Platform inserted in an small micelle.

Source code

Gromacs
check out the latest git version.

Additional data

sample.mdp is an example of a mdp file needed to generate an input tpr-file.

We tried g_membed on several test systems. You can download the pdb and topology file of a Beta-barrel overlapping a popc membrane and spc water system, to try it yourself.

A short manual is given in the help option of g_membed itself. For a more extensive manual see the appendix of our paper.