[gmx-users] g_sgangle and P atoms on the DNA molecule.
anna_gromacs at libero.it
anna_gromacs at libero.it
Tue May 14 14:38:03 CEST 2013
Dear users and experts,
my question is about the results given by the program g_sgangle,
when I try to calculate the angles between the two vectors defined by 3 consecutive P atoms, on the DNA structure (a single gro structure), the result is:
@ title "Angle between a_728_695 and a_695_662"
@ xaxis label "Time (ps)"
@ yaxis label "Angle (degrees)"
@TYPE xy
0 0.855195 31.2188
respectively time, angle and arccosine.
By literature is well known that viewing down the long axis of the DNA molecule, the P atoms are around in circle, and it would be numerically possible to calculate the angle between the two vector defined by 3 consecutive P atoms. If I'm right it is: (180° - 32.3°)= 147.7. So the value given by sg_angle is too low.
Where I'm wrong?
Many many thanks,
Anna
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