From: Axel Kohlmeyer (
Date: Wed Mar 19 2008 - 21:07:06 CDT

On Wed, 19 Mar 2008, Arneh Babakhani wrote:

AB> Hi all,

hi arneh,

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

how about using one of the moments of inertia as reference?


AB> Thanks,
AB> Arneh

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.