AMBER: the DNA conformation after engery minimization using NMODE

From: Xiaowei (David) Li <"Xiaowei>
Date: Mon, 10 Jan 2005 14:32:26 -0500

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.

Xiaowei Li

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Received on Mon Jan 10 2005 - 19:53:01 PST
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