it depends on what you want to learn, and if you are comparing to
experiment. If you look at CD, it's not a local measure of helix (not just
phi/psi pair). In that case I would suggest using DSSP in cpptraj, or
something like that. If you are comparing to NMR measures of helicity, such
as those using chemical shift, then it is a more local conformation and you
probably want phi/psi pairs.
We have some examples of helicity measures in an older article from my lab
Song, K., Stewart, J., Fesinmeyer, M. Andersen, N., Simmerling, C.,
“Structural Insights for Designed Alanine-rich Helices: Comparing NMR
Helicity Measures and Conformational Ensembles from Molecular Dynamics
Simulation”, Biopolymers, 89:747-760 (2008)
On Tue, Apr 29, 2014 at 11:06 AM, Suchetana Gupta <suchetana.gupta.gmail.com
> wrote:
> Dear AMBER users
> I have simulated a small peptide. It has a single alpha helix structure,a s
> visible from the VMD view. I would like to quantify the helix formation. I
> was thinking of looking at the dihedral angle between certain residues in
> the helix over the entire trajectory to get some idea. Is this correct? Can
> you suggest any other method to quantify the formation/time evolution of
> the helix?
> Thanks in advance for your help
> Suchetana Gupta
> Graduate Student
> Department of Biotechnology
> IIT Madras
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>
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Received on Tue Apr 29 2014 - 09:00:03 PDT
