[gmx-users] membrane protein simulation

[Tsjerk Wassenaar]

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" <brettliu123 at 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" <tsjerkw at 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" <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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