[gmx-users] membrane protein simulation
Brett
brettliu123 at 163.com
Sun Sep 13 12:00:00 CEST 2015
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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