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. > > > 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 >> >> ------------------------------ >> Windows Live: Make it easier for your friends to see what you’re up to on >> Facebook.<http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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