[gmx-users] Calculation of twist angle in gmx helix
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").
> Sridip Parui
> Senior research fellow
> Indian Association for the Cultivation of Science
> Kolkata-700032, India
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users