On Oct 23, 2009, at 9:45 AM, Amit Choubey wrote:
On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole <x.peri...@rug.nl>
wrote:
On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote:
On Thu, Oct 22, 2009 at 9:53 AM, S hv <sola...@hotmail.com> wrote:
Hi,
I am currently working with peptide/lipids interactions using the
martini force field. I want to built a bacterial membrane, so I
trying to find the
topology of the POPG lipid but until now without success.
In the martini_v2.0_lipids.itp file, the PG lipids are no included.
I have seen some works using the martini force field and POPG
lipids, e.g., " The molecular mechanism monolayer PNAS 105,
10803-10808", but they don't specify the topology of POPG lipids.
You can do this on your own just pull out the atomic structure of
DPPC and POPG from any website. Compare atomistic DPPC with the
Coarse Grained DPPC and it wont be hard to figure out the POPG CG
topology.
That is certainly not that easy. A lot of parameterizations efforts
have to be
involved.
No, thats easy because you are working with a coarse grained model.
There are are only few types of particles possible. The only tricky
ones are the head groups which the paper does mention.
If the bead type is given in the paper then the work is easier.
My point is that assimilate CG with simple is a big mistake!
BTW, the paper does give a short description about the topology of
POPG
The best is probably to ask the authors of that paper to share their
topology,
which they should.
I also tried in the martini web page, but I just found the
martini_v2.0_lipids.itp file.
Could anyone help me to find such topology?
Thanks a lot for your time,
Salvador
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