Pytraj for major groove width calculation and DNA bending?

29 March 2023 1 3K Report

Hi there !

Is there someone familiar with calculating nucleic acid parameters of MD simulations with pytraj?

I was just wondering which is the best way to calculate DNA bending using this and secondly why they say they calculated the major/minor groove width if they actually calculate the length of the grooves ?

(width would be around 12 Angstrom, but there parameters are around 19-20 so I am wondering what they actuaally calculate..?)

would be great if someone could help me out here :)

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