Dear All,
Suppose a membrane protein contains 10 trans-membrane helix, and thus the upper and lower part of the 10 trans- membrane are not horizontal, 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? 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? 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.