AMBER Archive (2004)

Subject: Re: AMBER: pbsa calculation on part of the molecule & nmode analysis

From: David A. Case (
Date: Thu May 20 2004 - 20:40:10 CDT

On Thu, May 20, 2004, S. Frank Yan wrote:
> However, in the normal mode analysis, it is usually not affordable to
> carry out the analysis for the entire complex. Do we just truncate the
> residues in the core region and carry out the normal mode analysis?

The whole question of how to generate good entropy estimates is still a matter
of current research. No really good scheme is known, especially for larger


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