Sugars are quite flexible and their puckers sample a wide range
during MD simulations. For that and your remaining questions
it would seem that you need to read some of the literature on
MD simulations of nucleic acids to get a better understanding
of the behavior of DNA. There are also examples of DNA-protein
calculations (we have some, as does Lennart Nilsson). One
place to start is with the CHARMM27 parameter papers; the
supplemental material (which is actually the entire paper)
can be obtained from my web page.http://www.pharmacy.umaryland.edu/faculty/amackere/param/force_field_dev.htm
Also, don't necessarily take a crystal structure as "truth." Depending on resolution etc.
they may not be able to properly assign the pucker.