[gmx-users] tilt angle

[Fa Hamedi]

Hi,
I am new in this mailing list and I have a question:
I haveve performed MD simulation of transmembrane protein using
Gromacs. Now, I want to calculate the angle of tilt of the
transmembrane protein against the bilayer normal. I know that I can
use

gmx helixorient but I don t know how should make index file?? My
protein is a dimer helix and has 61 residues. I don t know how choose
carbo alpha atoms for calculating tilt angle! can anyone help me??

Thank you.