Dear Tsjerk, Thanks for the reply. Will you please introduce to me sevral membrane builders whith results compatible with gromacs, especially on-line available membrane builders? Best regards. Brett
At 2015-09-13 17:45:52, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: >Hi Brett, > >So apart from the curvature of the membrane, there maybe the situation that >there's just more of the protein in one leaflet than in the other. You'll >need to account for that when embedding. Membrane builders typically check >for overlaps to take care of this. > >Cheers, > >Tsjerk >On Sep 13, 2015 11:37, "Brett" <brettliu...@163.com> wrote: > >> Thanks for the reply Tsjerk. In fact I am just wonding if the situation >> exist, i.e., for the 10th trans-membrane helices in the protein, the 8th >> and or 9th for example is/are a little shorter than the other several >> helices. Will you please give a comment on how to process this kind of >> membrane protein embeding in lipid Tsjerk? >> >> Brett >> >> >> >> >> >> >> >> At 2015-09-13 15:19:56, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: >> >Hi Brett, >> > >> >Say I'm designing this new type of truck. Because the earth it's riding >> >over is round, do you think I need to adjust the wheel positions on front >> >and back to match the curvature of the earth? >> > >> >Cheers, >> > >> >Tsjerk >> >On Sep 13, 2015 08:52, "Brett" <brettliu...@163.com> wrote: >> > >> >> >> >> Dear All, >> >> >> >> Suppose a membrane protein contains 10 trans-membrane helix, and as the >> >> cell membrane is round, the upper and lower part of the 10 trans- >> membrane >> >> are not horizontal as they are part of the rounded cell, will you please >> >> introduce to me how to make the lipid bilayer in curve to parallel the >> >> upper and lower part of the 10 tran- membrane? I only know we can pack >> the >> >> membrane protein into the lipid bilayer in the way the lipid bilayer >> would >> >> be perpendicular to the membrane protein. >> >> >> >> Yesterday I have posted a similar question but my post was not show in >> the >> >> post list. >> >> >> >> I am looking forward to getting your reply. >> >> >> >> >> >> Best regards. >> >> >> >> >> >> Brett >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -------- Forwarding messages -------- >> >> From: "Machtens, Jan-Philipp" <j.macht...@fz-juelich.de> >> >> Date: 2015-09-10 16:41:33 >> >> To: "gromacs.org_gmx-users@maillist.sys.kth.se" < >> >> gromacs.org_gmx-users@maillist.sys.kth.se> >> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer >> >> (martini) >> >> Hi Kathrin, >> >> if I remember correctly I once did something similar with g_membed >> -pieces >> >> ! >> >> >> >> Cheers, >> >> ==================================== >> >> Dr. Jan-Philipp Machtens >> >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4) >> >> Forschungszentrum Jülich, Germany >> >> Telefon: 02461 616467 >> >> ==================================== >> >> >> >> ________________________________________ >> >> Date: Thu, 10 Sep 2015 01:25:00 +0200 >> >> From: Kathrin Hadasch <kh...@web.de> >> >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer >> >> (martini) >> >> Message-ID: <55f0bfcc.7060...@web.de> >> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed >> >> >> >> Hey you all, >> >> I'm searching for a way to insert and embed multiple(!) copies of the >> >> same protein in a complex, presimulated membrane patch (all martini-cg). >> >> I've tryed lambada for insertion, but I couldn't get it to work with >> >> more than one protein. I've tried to translate the protein to a (4 4 0) >> >> vector with editconf in the lambada script, but I get following error: >> >> Modification of non-creatable array value attempted, subscript -6 at >> >> /home/lambada/modules/protein.pm line 281. >> >> For insertion via vmd, I have no clue how to generate a psf file for >> >> martini-lipids. >> >> Any suggestions how I could make it work? >> >> Best regards and thanks in advance, >> >> Kathrin >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------------------------ >> >> >> >> >> ------------------------------------------------------------------------------------------------ >> >> Forschungszentrum Juelich GmbH >> >> 52425 Juelich >> >> Sitz der Gesellschaft: Juelich >> >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >> >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >> >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >> >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >> >> Prof. Dr. Sebastian M. Schmidt >> >> >> >> >> ------------------------------------------------------------------------------------------------ >> >> >> >> >> ------------------------------------------------------------------------------------------------ >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? 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