[gmx-users] Aligning protein in bilayer with editconf

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 27 13:00:33 CET 2009

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.


> Regards,
> Anirban
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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


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