[gmx-users] membrane protein simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 23 07:10:20 CEST 2015

Hi Mostafa,

We have a complete simulation system of bacteriorhodopsin in the purple
membrane, which you can use as basis for your simulations if you want.


On Apr 22, 2015 10:08 PM, "Mostafa Javaheri" <javaheri.gromacs at gmail.com>

> Dear Justin
> I am going to simulate a homo trimer trans-membrane protein; Base on the
> crystallographic structures there is 7 phosphatidyl glycerol phosphate
> (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3
> -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
> extracellular side of membrane. In the membrane protein tutorial of gromacs
> 1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced as
> the standard lipids, so should I treat PGPs and glycolipids as ligands and
> going through protein ligand complex tutorial?
> Or treat glycolipids as ligands, continue the membrane protein tutorial and
> use DPPCs instead of PGPs?
> Is it OK if I replace PGP with DPPC from the standpoint of simulation?
> Sincerely
> --
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