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.grom...@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 > -GalpĪ²1-6ManpR1-2GlcpR-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-requ...@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-requ...@gromacs.org.