[gmx-users] g_helix

[Justin A. Lemkul]

Carla Jamous wrote:
> Hi everyone,
> 
> Please I need some advice concerning g_helix:
> 
> It's the first time I use this analysis. In the manual, it says:
> g helix computes all kind of helix properties. First, _the peptide is 
> checked to find the longest helical part._
> This is determined by Hydrogen bonds and Phi/Psi angles. That bit is 
> fitted to an ideal helix around the
> Z-axis and centered around the origin. Then the following properties are 
> computed:
> 
> However, when I do the following:
> 
> g_helix -s topol.tpr -f traj.xtc -n index.ndx -cz x.gro -co y.gro
> 
> I can't see anywhere if the program tells me which part is the longest 
> helical part. And I don't understand what are x.gro & y.gro
> 
> Please can anyone tell me more about this option, because it's not very 
> clear in the manual.
> 

The source code explains these options:

-cz: "Helix fitted to Z-Axis"
-co: "Weighted and Averaged conformation"

Based on the output .xvg files, you should be able to reconstruct the longest 
helix, although you should probably have an idea of what this is prior to 
running the analysis, anyway.

-Justin

> Thanks
> 
> Carla
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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