[gmx-users] Aligning protein in bilayer with editconf

Anirban Ghosh reach.anirban.ghosh at gmail.com
Tue Oct 27 12:36:33 CET 2009


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.


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