[gmx-users] membrane protein simulation

[Brett]

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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