VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Wed Mar 19 2008 - 20:24:38 CDT

Hi all,

I was wondering if there's a good way to calculate the tilt angle of a
non-helical peptide (in a membrane).

I thought I could do so by defining a vector connecting the first and last
C-alpha atoms, and measuring the angle between that vector and the
z-normal. But then if there are significant conformational changes in my
peptide during the simulation, this defined vector (and angle calculated
from it) may not be a good reflection of the peptide tilt, right? So
would it be better to define a vector containing all of the C-alpha atoms
in the peptide (with some fitting of course)???

Thanks,

Arneh