[gmx-users] Protein Orientation

[sunny mishra]

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

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?

Thanks,

Sunny