How can I calculate the torsion angles of a specific residue side chain over MD trajectory in VMD?

07 July 2018 1 2K Report

I performed a 100 ns MD of a protein in an organic solvent and I want to calculate the change in torsion angles of a specific residue side chain over the simulation. is there any script to do that ?

Vishal Pandya

You could use the following two links to help you out using python to calculate the torsion angle.

https://stackoverflow.com/questions/20305272/dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python

http://azevedolab.net/resources/dihedral_angle.pdf

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