[gmx-users] How to calculate the angle between side chains and helical axis
duartenl at yahoo.com.br
Thu Mar 15 10:02:39 CET 2007
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?
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