[gmx-users] membrane protein simulation

Brett brettliu123 at 163.com
Sun Sep 13 08:51:35 CEST 2015

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.


-------- Forwarding messages --------
From: "Machtens, Jan-Philipp" <j.machtens at fz-juelich.de>
Date: 2015-09-10 16:41:33
To:  "gromacs.org_gmx-users at maillist.sys.kth.se" <gromacs.org_gmx-users at 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 !

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 <khada at web.de>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Multiple membrane proteins in complex bilayer
Message-ID: <55F0BFCC.7060104 at 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
Any suggestions how I could make it work?
Best regards and thanks in advance,

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

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