I hope you have a good time.
Recently, I am analyzing a 12-mer DNA (MD trajectory) with N1-methyladenine in ADE16 which adopt a syn conformation and form Hoogsteen base pair with THY9. When I use X3DNA to analyzing it, I find some parameters are kinda wired. I analyze the base pair parameters in 3-22, 4-21, 5-20, 6-19, 7-18, 8-17, 9-16, 10-15 bps and step and helical parameters in 3-4, 4-5, 5-6, 6-7, 7-8, 8-9. 9-10.
First, let's just look at the analysis of first snapshots in this MD simulation (A6me_50ps.pdb).
(1) Base pair parameters: There are clear differences in the 9-16 step (HG base pairs) like shear, stretch and especially opening.
(2) Step and helical parameters: There are some sort of difference in tilt, twist, inclination.
My first question is: Where are these difference come from. I know that you define a coordinate frame for idealized DNA before analyzing, but is this definition also applied to Hoogsteen base pair? Do we need to redefine a coordinate frame for Hoogsteen base pair when we want to analyzing base pair parameters (or just use the idealized coordinate frame)? Are the step and helical parameters also intrinsically influenced by the coordinate frame of Hoogsteen base pair so we should expect to see these difference?
I also attach the full MD trajectory analysis for your reference. Some parameters' error bar is very large like x-displacement, y-displacement, that could be due to some MD issue which I plan to double check that.