From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 19 2008 - 21:52:58 CDT

On Wed, Mar 19, 2008 at 10:37 PM, Arneh Babakhani
<ababakha_at_mccammon.ucsd.edu> wrote:
> Ok, but how would I define the axis of rotation?

by diagonalizing the inertia tensor. see:

http://en.wikipedia.org/wiki/Moment_of_inertia

just pick the eigenvector that is closest to orthogonal
with the membrane normal.

a.

>
>
>
>
> > 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>
> > 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?
> >
> > cheers,
> > axel.
> >
> >
> > AB>
> > AB> Thanks,
> > AB>
> > AB> Arneh
> > AB>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > 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.
> >
>
>
> --
> Arneh Babakhani
> McCammon Lab
> Department of Chemistry & Biochemistry
> University of California at San Diego
> 9500 Gilman Dr MC 0365
> La Jolla, CA 92093-0365
> (619)895-6540
> (858)534-4974 (FAX)
> ababakha_at_mccammon.ucsd.edu
> http://mccammon.ucsd.edu/~ababakha/
>
>

-- 
=======================================================================
Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
 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.