I don't know if this helps you, but there is a membrane plugin for VMD which you can download for free. I've used this to insert proteins in membranes and then use namd to run MD. I don't know what steps are involved to make this structure compatible with GROMACS.
http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/ On Sat, May 2, 2009 at 7:46 AM, Anirban Ghosh <[email protected]> wrote: > Hi ALL, > > > > I have a protein pdb file. I want to put this protein molecule in a lipid > bilayer using GROMACS. I shall be glad if anyone can kindly tell me how to > build a lipid bilayer in GROMACS and how to embed the protein in it to get > the final pdb of the entire system. Thanks a lot. > > > > Regards, > > > > > > Anirban Ghosh > > Grade Based Engineer > > Bioinformatics Team > > Scientific & Engineering Computing Group > > Centre for Development of Advanced Computing > > Pune, India > > > > Anirban Ghosh > Grade Based Engineer > Bioinformatics Team > Centre for Development of Advanced Computing (C-DAC) > Pune, India > > > ________________________________ > Cricket on your mind? Visit the ultimate cricket website. Enter now! > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org _______________________________________________ gmx-users mailing list [email protected] http://www.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
