AMBER Archive (2005)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 10 2005 - 21:56:25 CST

> 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.

In this case, yes.

> I would like to know whether it is always necessary to do so.

It depends on the input coordinates.

You might try some low-temperature (10K) dynamics instead of
minimization.

Bill
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