Hi,
> I know that a larger value indicates a larger separation between base pairs
That's not strictly correct; the base pair parameters (Opening,
Propeller, Buckle, etc.) have specific geometric definitions. In the
case of Opening, it is defined as the angle between the base reference
Y-axes *with reference to the Z-axis*. In the case of parallel strands
of DNA, the Z-axis of one base is flipped relative to what it would be
when the bases are anti-parallel, so the values for Opening are
similarly "flipped".
The procedure CPPTRAJ uses is the same one found in 3DNA - I'll paste
the relevant references below. If you find that the CPPTRAJ results
deviate significantly from those produced by 3DNA (or some other NA
analysis code) please let me know. Hope this helps!
-Dan
References:
- XJ Lu and WK Olson. 3dna: a software package for the analysis, rebuilding
and visualization of three-dimensional nucleic acid structures. NUCLEIC
ACIDS RESEARCH, 31:5108–5121, 2003.
- M.S. Babcock, E.P.D. Pednault, and W.K. Olson. Nucleic Acid Structure
Analysis. J. Mol. Biol., 237:125–156, 1994.
- Wilma K. Olson, Manju Bansal, Stephen K. Burley, Richard E. Dickerson,
Mark Gerstein, Stephen C. Harvey, Udo Heinemann, Xiang-Jun Lu,
Stephen Neidle, Zippora Shakked, Heinz Sklenar, Masashi Suzuki, Chang-
Shung Tung, Eric Westhof, Cynthia Wolberger, and Helen M. Berman. A
standard reference frame for the description of nucleic acid base-pair geometry.
J. Mol. Biol., 313:229–237, 2001.
On Thu, Jan 2, 2025 at 7:35 AM Jing Qu via AMBER <amber.ambermd.org> wrote:
>
> 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 - 08:30:02 PST
