AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: David A. Case (
Date: Wed Apr 29 2009 - 12:56:28 CDT

On Wed, Apr 29, 2009, waleed zalloum wrote:
> I am using sander to calculate the 3D structure of a conjugate of
> oligopeptide and oligonucleotide. I start the calculation at 1000K. in
> the output file, the nucleotide bases are not planner and amino groups
> are distorted. My question is, how could I constrain the amino groups
> and the planarity of nucleotide bases?

Such groups will not be planar at 1000K, but it is not clear why they
need to be. You could add in specific torsion restraints to keep groups
planar if you want. There is no pre-programmed way to do this, so some
hand-work would be involved. But are you sure this is really what you want to


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