# Re: [AMBER] How to calculate the tilt angle of TM helix

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Sat, 10 Aug 2019 09:25:38 -0400

Hi,

Like Callum mentioned, 'vector principal x' will get you the primary
principal axis (i.e. the axis with the highest eigenvector - cpptraj
uses principal X > Y > Z by convention for historical reasons). That
usually works, but you do have to sometimes be careful about sign
flips; in that case you can also get an approximate vector by
calculating the vector between the center of mass of the residues at
the beginning and the end of the helix - I usually use 3 residues
which are ~3 from each end to account for any end-terminal fraying, so
e.g. with an 18 residue helical peptide I'd use residues 4-6 and
13-15. To get the vector of the membrane itself you can either just
use the Z axis (if your membrane is aligned that way and doesn't
really move a lot) or use 'vector corrplane' to get the vector
orthogonal to the plane that passes through the lipids (or lipid

parm myparm.parm7
trajin mytraj.nc
# Peptide vector (molecule 1)
vector VA ^1:;4,5,6.N,CA,C ^1:;13,14,15.N,CA,C
# or use 'vector VA principal X ^1'
# Membrane vector
vector VM corrplane :DOPC
# Angle of peptide to membrane
vectormath vec1 VM vec2 VA out vector.agr name AngleA dotangle

Hope this helps,

-Dan

On Fri, Aug 9, 2019 at 4:18 AM Maria Bzówka <m.bzowka.tunnelinggroup.pl> wrote:
>
> 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?
>
> Do you have any suggestions?
>