VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Wed Apr 06 2011 - 16:23:29 CDT

Dear VMD users:

I want to obtain a measure of the orientation of a small a-helix with
respect to the vector normal to a membrane, i.e the z axis.
My problem consist of a homo-hexameric transmembrane-channel in wich a small
10 residues long a-helix from each monomer points towards the center of the
channel. I want to study how the orientation of this small helix changes
during a simulation and compare Wt against some mutants. Vi visual
inspection there seem to be differences in the orientation of the helix with
respect to the z o r channel axis. I want to quantify the orientation. I was
thinking of using the order parameter P1 and P2 that allows one to calculate
the perpendicular or parallel orientation of molecules. The problem is:

1)How do I define the small helix as a vector? Should I use it´s dipole
moment for example?

2) How do I measure the angle between the vector formed by the helix and the
z axis?

Thanks..

Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.