I have simulated a protein molecule. I need to calculate the side chain torsion angles along with main chain torsion angles for all/or any particular residue(s). I am trying to use a tcl script.
There is a bioinformatics app known as VMD (Visual Molecular Dynamics) which can be downloaded from: http://www.ks.uiuc.edu/Research/vmd . If your preference is for Tcl-implemented programs, then you'll be pleased to know that this VMD application has a Tcl/Tk interface and there is a fairly thorough tutorial on how to use VMD at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972669/ .
I have written a python script to compute torsional angles which is shared on my GitHub here:
https://github.com/jamie-alnasir/artemis/blob/master/Artemis.py
Alternatively, if you prefer a visual tool, my molecular viewer Zeus (for Windows) is able to load quite a few molecular file formats and compute torsional angles on PDB structures:
http://www.al-nasir.com/portfolio/zeus/
In Vmd, use this command:
set dihedlist [measure dihed {atom1 atom2 atom3 atom4} frame all]
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