You can use cpptraj and the vector command with type "principal" to get the principal axes of inertia of your helix.
Best,
Callum
-----Original Message-----
From: Maria Bzówka <m.bzowka.tunnelinggroup.pl>
Sent: Friday, August 9, 2019 4:18 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] How to calculate the tilt angle of TM helix
Dear All,
During the simulation I can see quite a lot of changes in the position of my TM helix immersed in the lipid bilayer, so I would like to calculate the tilt angle between the transmembrane helix principal axis and the vector along the Z-axis. However, I'm not so sure how to do that...
As a principal axis of TM helix I mean the C-alpha atoms from the helix (which is 30 residues) and I suppose that I should somehow use the vector command from cpptraj?
