[gmx-users] Calculation of twist angle in gmx helix

Mark Abraham mark.j.abraham at gmail.com
Tue May 21 09:19:25 CEST 2019


On Tue, 21 May 2019 at 08:56, Sridip Parui <paruisridip at gmail.com> wrote:

> Dear Experts,
> When "gmx helix" is run, we obatin severals outputs, one of them helix
> "twist angle". I do not know how the paramter is being calculated. I
> manually calculated the angle between succesive C-Alpha atoms, between
> succesive backbone carbonyl C atoms and also between successive backbone N
> atoms. But none of them is matching with the "gmc helix" generated values.
> I want to take "number of residues per turn" as an order paramter. For
> that, I need to calculate twist angle.
> How exactly "twist angle" is calculated in "gmx helix"?
> References with clear elaboration will be appreciated.

Unfortunately there's only really the code, e.g.
it is clear that the angle is that subtended by successive alpha-carbon
atoms (projected to a common Z coordinate) to the ideal helical axis (along
Z) to which the actual helix has been fitted (see "gmx help helix").


With regards,
> Sridip Parui
> Senior research fellow
> Indian Association for the Cultivation of Science
> Kolkata-700032, India
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