Put your protein file in TMDET and it will align the protein for you perpendicular to Z axis and also the protein will be at origin in that case then you can use geom_center script provided in VMD to put the lipid in the origin and move it towards the protein. Hope it helps
On Tue, Oct 27, 2009 at 8:00 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I am facing a strange problem, while aligning a protein molecule in a >> lipid bilayer. I am using the center coordinates of the lipid .gro file >> (values in the last line of .gro) with -box option of editconf to properly >> align the protein with the bilayer. Now the problem is that the protein is >> in the middle of the bilayer, but it is parallel to the bilayer. I need to >> rotate it by 90 degrees to make it perpendicular with the bilayer (which is >> normal with any protein-lipid complex.). But I am not able to do this with >> editconf or any other command. Please suggest how to do this. Any suggestion >> is welcome. Thanks a lot. >> >> > So you're saying that editconf -rotate is not working? That's what it's > designed to do. If you think something is broken, at least provide the > command you're issuing so we can see if there's something wrong with it. > > -Justin > > Regards, >> >> Anirban >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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