[gmx-users] membrane protein simulation

[Mostafa Javaheri]

Hi Tsjerk,

Yes, it would be very helpful. thanks for your help.

Best regards,

Mostafa

On Thu, Apr 23, 2015 at 9:40 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Mostafa,
>
> We have a complete simulation system of bacteriorhodopsin in the purple
> membrane, which you can use as basis for your simulations if you want.
>
> Best,
>
> Tsjerk
> On Apr 22, 2015 10:08 PM, "Mostafa Javaheri" <javaheri.gromacs at gmail.com>
> wrote:
>
> > Dear Justin
> > I am going to simulate a homo trimer trans-membrane protein; Base on the
> > crystallographic structures there is 7 phosphatidyl glycerol phosphate
> > (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or
> 3-HSO 3
> > -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
> > extracellular side of membrane. In the membrane protein tutorial of
> gromacs
> > 1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced
> as
> > the standard lipids, so should I treat PGPs and glycolipids as ligands
> and
> > going through protein ligand complex tutorial?
> > Or treat glycolipids as ligands, continue the membrane protein tutorial
> and
> > use DPPCs instead of PGPs?
> > Is it OK if I replace PGP with DPPC from the standpoint of simulation?
> > Sincerely
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>