[gmx-users] membrane protein simulation

[Mostafa Javaheri]

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