[gmx-users] membrane protein simulation
Tsjerk Wassenaar
tsjerkw at gmail.com
Sun Sep 13 12:29:41 CEST 2015
Hi Brett,
If you mean an online server, then probably the CHARMM-GUI was made for
you. If you mean downloadable, then you can try inflategro or insane
(coarse-grained). In addition, Gromacs comes with g_membed integrated.
Cheers,
Tsjerk
On Sep 13, 2015 12:00, "Brett" <brettliu123 at 163.com> wrote:
> Dear Tsjerk,
>
> Thanks for the reply. Will you please introduce to me sevral membrane
> builders whith results compatible with gromacs, especially on-line
> available membrane builders?
>
> Best regards.
>
> Brett
>
>
>
>
>
>
>
> At 2015-09-13 17:45:52, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
> >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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