[gmx-users] Question: Fw:Re: Multiple membrane proteins in complex bilayer (martini)

[Brett]

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.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 !

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


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