AMBER Archive (2005)

Subject: AMBER: Amber 8: all_nucleic94.lib nucleotide geometry

From: Angela Liu (angela_ambermail_at_yahoo.com)
Date: Wed Aug 17 2005 - 17:42:03 CDT

Dear Amber developers and users,

When I examine the geometries of the DNA nucleotides
from the $AMBERHOME/dat/leap/lib/all_nucleic94.lib
file, I found that the bases are not perfectly planar.
 For instance, the H8 atom of Adenine and the H6 atom
of Thymine are out of the plane by 2-3 degrees (from
perfect 0 or 180 dihedral angles). For room
temperature molecules, such small variation from
perfect planarity is reasonable and expected, but the
average position of the hydrogen atoms is usually in
the molecular plane.

My question then is what experimental evidence is
there that can backup such arrangements of the
hydrogen atoms in the standard library files? Why
wouldn't completely planar structures be used in these
library files?

Thank you very much for your time and help!

Angela

                
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