[gmx-users] topologies for POPE and DMPE

Thomas Piggot t.piggot at soton.ac.uk
Mon Oct 17 12:07:04 CEST 2011

Hi Roy,

PE lipids are less frequently used than PC ones and there are fewer 
topologies available. Also it has been shown that using the Berger PC 
lipid topologies (the most frequently used united-atom PC lipids) and 
simply changing the CH3 atoms in the head group to H is not a good 
approach for PE (de Vries et al. DOI: 10.1021/jp0366926 is I think the 
first mention of this).

Other PE topologies I am aware of are either the all-atom CHARMM (27 or 
36) lipids or there are two united-atom GROMOS PE topologies:

The first is the GROMOS43A1-S3 force field which has a POPE topology 
(you can download this from the contributions section on the GROMACS 
website). I have simulated a POPE membrane using these parameters before 
with no problems.

The second (and here is a shameless plug for some of my work, sorry!) is 
a GROMOS53A6 based PE described in a paper we have just got accepted 
into J. Phys. Chem B (http://dx.doi.org/10.1021/jp207013v). The 
supplementary information for this paper (which is not yet available) 
has an analysis/validation of POPE and DPPE membrane using these 
parameters which are based upon the PC topologies of Kukol (DOI: 
10.1021/ct8003468) and Chandrasekhar (DOI: 10.1007/s00249-002-0269-4). 
If you (or anyone else) wish to use these PE topologies send me an email 
off-list and I can let you have them. I have not tested DMPE yet but I 
would imagine it should be similar to DPPE and you can also make a DMPE 
bilayer from a DPPE one by simply removing two CH2 groups from each 
lipid tail and equilibrating the new membrane.



Roy Lee wrote:
> Dear all,
> I would like to simulate my protein in a lipid bilayer using gromacs 
> 4.5.4, and a forcefield of gromos96. However i don't have the topologies 
> files for lipid bilayer for POPE and DMPE. Anybody knows where can i get 
> the topologies file for POPE and DMPE ?
> Any help is much appreciated.
> Thanks a lot!
> Roy

Dr Thomas Piggot
University of Southampton, UK.

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