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From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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>
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> 

-- 
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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
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If you make something idiot-proof, the universe creates a better idiot.