[gmx-users] topologies for POPE and DMPE
t.piggot at soton.ac.uk
Mon Oct 17 12:07:04 CEST 2011
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!
Dr Thomas Piggot
University of Southampton, UK.
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