[gmx-users] Calculation of helicity of alpha-helix which is parallel to X-axis

Justin Lemkul jalemkul at vt.edu
Sat Apr 27 18:27:17 CEST 2013

On 4/27/13 11:43 AM, Sujit Sarkar wrote:
> Hi,
> I want to calculate helicity of an alpha-helix which is parallel along
> X-axis. But, during usage of g_helix command its manual showing it will
> calculate helicity of alpha-helix which is parallel to Z-axis.
> So, please tell me the solution.

Use trjconv and editconf to realign the helix with the z-axis.  If you're only 
looking for secondary structure over time, do_dssp is much easier.  If you want 
all the properties that g_helix measures, you will have to realign it.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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