Hi,
I'm using CPPTRAJ to analyze simulations of parallel strand DNA and get
parameters via "nastruct". When concentrating on the parameter "open", I
will get values around -170 and 170. I know that a larger value indicates a
larger separation between base pairs, but apparently my structure isn't
split wide open. I think usually when structures are not split, the values
should near 0. I'd like to know what the logic is for AMBER to calculate
"opening"? I'm guessing that the value may be due to the fact that I'm
analyzing parallel strand. Do I just need to subtract the value from 180
(by which I mean turn the value to concentrate around 0), or do I then go
to the absolute value? Does the negative value make sense? Or is there some
adjustment I need to make in the code I am analyzing for parallel strand?
Thanks,
Jing
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Received on Thu Jan 02 2025 - 05:00:02 PST
