[gmx-users] How to calculate the angle between side chains and helical axis

[Afonso Duarte]

Dear All,

I have performed a MD simulation of a helical peptide in a solvent box.

Now I am interested on determining the angle between the helix axis and the side chain of some residues (defined by the vector form Cb to the terminal heavy atom of each residue). 

I am trying to do so using g_bundle... is this a good aproach? 
My problem with g_bundle is that I can define the top and bottom of the helix axis, but how can I define the other axis for each residue?

Thanks!

Cheers

Afonso

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