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I need to calculate the dihedral angle between C20 and C19, as well as between C19-C18. enter image description here Can someone help me choosing the right combination? I have used the following one: C18C19C20C23 for the first angle and C20C19C18N7 for the second one. (I am using Maestro software and I am trying to make an energy plot for chi and psi angles). However I am not sure if I should use instead the following combinations: C23C20C19C18 and N7C18C19C20. Does it make any difference? Thank you!

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  • $\begingroup$ It makes a difference. Phi and psi are defined for polymers of alpha-amino acids, which this molecules is not. "The phi-angle (φ) - around the N-Cα bond. The psi-angle (ψ) - around the Cα-C bond" (www3.cmbi.umcn.nl/wiki/index.php/Torsion_angle). $\endgroup$ Jun 28 '20 at 23:40
  • $\begingroup$ it is not about phi and psi angles. this is not a protein. (I mentionned psi and chi angle). this is nelfinavir $\endgroup$
    – marilu
    Jun 29 '20 at 5:12
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The picture shows how the dihedral angle $\psi$ is defined. You will need to be familiar with vectors to be able to calculate this angle; $\cos(\psi)=m\cdot n/(|m||n|)$ where the vectors are shown in the figure, vector $m$ is perpendicular to $a$ and $b$, $m=a\times b=|a||b|\sin(\gamma)$ and $n=b\times c$.

vectors

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  • $\begingroup$ Thank you a lot!Fortunately I am using a software, so I will not make the calculations by myself. I just need to select the right 4 atoms. Could you tell me your opinion about the selection of the atoms? I have written in the question the atoms that I have selected. Thank you!! $\endgroup$
    – marilu
    Jun 29 '20 at 7:35
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    $\begingroup$ It is up to you but its either 18-19-20-22 or 18-19-20-23 and the second 7-18-19-20 $\endgroup$
    – porphyrin
    Jun 29 '20 at 13:32
  • $\begingroup$ Thank you so much for your answer!! I really appreciate it! $\endgroup$
    – marilu
    Jun 29 '20 at 15:11
  • $\begingroup$ hoowever I cannot understand why in the the angle C20-C19 we do not begin from C22 and finish to C18 and in the angle C19-C18 we do not begin from C20? Thank you! $\endgroup$
    – marilu
    Jun 29 '20 at 16:28
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    $\begingroup$ you could start at either end. $\endgroup$
    – porphyrin
    Jun 30 '20 at 8:42

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