Hi Pramod,
Please keep all general queries and questions on the GROMACS mailing list.
For CHARMM27, POPC can be found as an rtp entry. This means a topology
can be generated using pdb2gmx. It is easiest if you do this using one
POPC lipid and then make an itp from the top. A CHARMM POPC bilayer can
be downloaded from the internet
(http://terpconnect.umd.edu/~jbklauda/research/download.html).
Cheers
Tom
ram bio wrote:
Dear Dr.Tom,
This is in response to the your message regarding the lipid bilayers
for MD simulation. I have a protein and ligand complex to be simulated
in lipid bilayer. Do, you have POPC structure and itp files
parameterised by CHARMM 27 FF.
Regards,
Pramod
On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot <[email protected]> wrote:
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.
Cheers
Tom
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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--
Dr Thomas Piggot
University of Southampton, UK.
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