AMBER Archive (2005)

Subject: AMBER: the DNA conformation after engery minimization using NMODE

From: Xiaowei (David) Li (xl3a_at_virginia.edu)
Date: Mon Jan 10 2005 - 13:32:26 CST

Dear David and amber users:
      I just checked the DNA conformation after energy minimization
using NMODE recently. I found that the DNA strucutre had been changed a
lot when miminzing the potential engergy. Although the minimized DNA
looks still likedouble helix strucutre, the base pairs at the two ends
of helix chain are totally seperated. Do I need to restraint the base
pairs at the ends of helix chain in order to keep it unchanged widely.
I would like to know whether it is always necessary to do so. Thank
you in advance.

Best,
Xiaowei Li

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