VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Wed Mar 19 2008 - 21:37:45 CDT

Ok, but how would I define the axis of rotation?

> 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/