Re: How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations

From: Jérôme Hénin (
Date: Fri Jan 13 2017 - 02:57:13 CST

Hi Lucas,

For that work, the reference conformations were not strictly speaking
"ideal" (if I wrote that, it was a poor choice of words). They were local
energy minima of that particular peptide under those particular conditions,
and I selected them from ABF trajectories using different coordinates.

If you are simulating the very same system, I will gladly share the files I
used (perhaps off-list) - however they don't have any general value: some
of them are rather idiosyncratic of that peptide.


On 13 January 2017 at 03:09, Jessen Lucas <> wrote:

> Dear all,
> I am reading "Exploring Multidimensional Free Energy Landscapes Using
> Time-Dependent Biases on Collective Variables", in there, I want to plot
> the free energy landscape, I saw there use three collective variables, the
> rmsd with respective to the ideal alpha-helical, ω-shaped γ-turn, and
> turn/310-helix conformations, respectively. My question is how to set this
> three collective variables in NAMD? I do not know what the conformations of ideal
> alpha-helical, ω-shaped γ-turn, and turn/310-helix.
> Thanks for any kindly suggestion.
> Lucas

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