[gmx-users] E. coli's Inner Membrane Lipid Selection

Jonathan Saboury jsabou1 at gmail.com
Sat Feb 18 22:12:20 CET 2017

Hello all,

I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui
to build the membrane but having difficulty deciding on membrane

AcrB is a protein in E. coli's inner membrane: http://www.nature.com/nature/

Based on the below literature, I have chosen the following membrane: PYPE
70%, PYPG 14%, DPPS 8%, TYCL2 8%.

Characterization of the Escherichia coli membrane structure and function
during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/

My two main questions are:
1.) Does lipid choice affect MD simulation much? I'm using charmm36
2.) Does my lipid selection make sense? If not, why and what would you use?

Thank you for your time!! :-)

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