[gmx-users] Aligning protein in bilayer with editconf

[sunny mishra]

Put your protein file in TMDET and it will align the protein for you
perpendicular to Z axis and also the protein will be at origin in that case
then you can use geom_center script provided in VMD to put the lipid in the
origin and move it towards the protein. Hope it helps

On Tue, Oct 27, 2009 at 8:00 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> I am facing a strange problem, while aligning a protein molecule in a
>> lipid bilayer. I am using the center coordinates of the lipid .gro file
>> (values in the last line of .gro) with -box option of editconf to properly
>> align the protein with the bilayer. Now the problem is that the protein is
>> in the middle of the bilayer, but it is parallel to the bilayer. I need to
>> rotate it by 90 degrees to make it perpendicular with the bilayer (which is
>> normal with any protein-lipid complex.). But I am not able to do this with
>> editconf or any other command. Please suggest how to do this. Any suggestion
>> is welcome. Thanks a lot.
>>
>>
> So you're saying that editconf -rotate is not working?  That's what it's
> designed to do.  If you think something is broken, at least provide the
> command you're issuing so we can see if there's something wrong with it.
>
> -Justin
>
>  Regards,
>>
>> Anirban
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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