[AMBER] Querry about puckering

From: Aparna P <aparnaspap.gmail.com>
Date: Wed, 21 Jan 2015 12:06:29 +0530


In an MD simulation performed on a modified DNA sequence, although the
starting structure sugar puckers are mostly in c2'endo conformation. Upon
dynamics there are some variance in puckering.
On interpreting the results, i would like to know "does South region means
exclusively C2'endo or does it involves immediate neighbors like C1'exo and
the intermediate O4'endo..
  Also sir, I would like to know if there is any direct relation between
h-twist and h-rise. Is there any significant difference between h-rise and
L-rise. it feels that, in some papers, though rise of standard BDNA and
ADNA were quoted with helical values but values got from theoretical
calculations were L-rise.

Thanking you

Aparna P
Research Scholar
School of Pure And Applied Physics
M.G University
AMBER mailing list
Received on Tue Jan 20 2015 - 23:00:02 PST
Custom Search