[gmx-users] Protein Orientation

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 19 04:18:00 CEST 2009

sunny mishra wrote:
> Dear All,
> I am following the tutorial given by justin and have question
> regarding the orientation of protein. Tutorial says that orient the
> protein along z axis using editconf -princ command followed by the
> rotation along y axis. My question is that when I use the editconf
> -princ command, does it automatically orient the protein along z axis
> because i gave the following command and I wasn't sure if I am correct
> or not, the command is: editconf -f protein.gro -princ -o
> protein_z.gro

It depends on your Gromacs version.  As stated in the tutorial:

"The .pdb file was oriented along the z-axis using editconf -princ, followed by 
a rotation about the y axis. Note that in Gromacs-3.3.x, the -princ option 
oriented the long axis of the structure (in this case, the helix axis) along the 
z-axis by default, but this option has changed as of Gromacs-4.0.4, which 
orients the long axis along the x-axis. If you want to skip the construction of 
this peptide, the properly oriented structure can be found here."

> Please correct me if I am wrong and also what do you mean when you say
> followed by the rotation along the y axis, by how much angle do i need
> to rotate?

What angle do the coordinate axes make with one another? :)


> Thanks,
> Sunny
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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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