[gmx-users] membrane protein simulation

[Tsjerk Wassenaar]

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" <brettliu123 at 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.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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