> Hello Gromacs Users, > > I would like to run a simulation of a trimer in a DPPC membrane. I > really like the elegant solution that inflategro script offers, > however I'm afraid I won't be able to use it, because I need to have > lipids in a small space between the monomers right in the center of > the box and these will certainly get deleted during the whole > procedure. I also need to keep the waters that come with the structure > of the protein. > Do you have any idea how I can elegantly embed my trimer in a > membrane, possibly using somehow modified inflategro? > > Christopher > We developed a new gromacs tool, g_membed, to insert a protein into a bilayer. It works different than inflategro. Instead of inflating and deflating the bilayer in this approach the protein is slowly grown from a narrowed protein to its full size during a short md run.
The paper describing this tool has just been accepted by J. Comp. Chem. As soon as we have a doi we will merge it to the git version. For now you can download a version from our website and compile it yourself: http://wwwuser.gwdg.de/~ggroenh/membed.html With this tool you can also keep the crystal waters (or for that matter anything from the crystal structure you want to keep). If you need three proteins in the bilayer you can insert them one at the time. For a more elaborate manual type g_membed -h. Cheers -- Dr. Maarten G. Wolf Max-Planck-Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11 37077 Goettingen Germany Phone: (+49) (551) 201 - 2320 Fax: (+49) (551) 201 - 2302 Email: [email protected] -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
