2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-phosphomethyl

GROMOS53a6 Gromacs by XYZ

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Lipid 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-phosphomethyl (DPhPGP-Me)
Pubchem CID:4469581
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario

This is an Archaeal lipid found in the Purple Membrane

I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer (all done with a bit of editconf!). You then have a more or less regular looking bilayer- add water, ~40 waters per lipid molecule to the box (solvating the tails of the lipid aswell) then simulated for 20 ns.

Bilayer file is at the end of a 20ns run


D'Rozario R, (2009), [no doi], [no pubmed id] Notes: (unpublished)
Primary Experimental


Version 1
PGP-Me.itp 7745c7f7883c6b48dccaeaf1cfc83e3336821578
ffG53a6bonrob.itp 36493d8950b1c75ca0426acd1e5863a04b1382d8
ffG53a6nbrob.itp 4348ee99fdc3e56c2c0ea8ecb7b0e1498ccc53c5
ffG53a6rob.itp 94edd1010f2dee31d67b898d7516a7ca73d8f5bc
PDB structure
DPhPGP-Me.pdb 2e8114d2610b91e40ec0c82ae3a29ed8ac3a9642
Bilayer structure
end-20ns-PGPG-ME.pdb a97f14d751a05e532ae3577ffe99566e4993f90a