Dear list,
I have begun to do some analysis of the Dickerson dodecamer using the
nastruct command in cpptraj in Ambertools 12.
The DNA was constructed as canonical B-DNA using NAB, and equilibrated
carefully in explicit water with the 11-step procedure as done in
Cheatham, et al., Refinement of the AMBER Force Field for Nucleic Acids:
Improving the Description of a/g Conformers.
Analysis using nastruct of the first 5ns of the production run gives a
file where some of the frames are missing all the parameter data for one
of the base-pairs; for example all base-pair info might be present for a
given frame except that a line for base-pair 6-19 is completely missing.
Since nastruct claims to give identical results to 3DNA, but I have never
used 3DNA, I am not sure if this is normal behavior or not, and I have no
idea on how to interpret it.
Since sometimes NO information is given for a particular base-pair in a
trajectory frame, and visual inspection of the frames in question in VMD
does not show any gross abnormalities of the base-pair, I have no clue as
to what is causing nastruct to provide no information for that particular
base-pair.
I originally thought that the problem was simply fraying of the ends of
the dodecamer, but the problem is happening in base-pairs that are clearly
not near the ends of the dodecamer.
Is missing information for internal base-pairs normal? What would cause
that? How is this to be interpreted?
Thanks very much for your help,
Dean
--
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
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Received on Thu May 31 2012 - 12:30:03 PDT
