AMBER Archive (2009)

Subject: Re: [AMBER] Dyndom

From: Carlos Simmerling (
Date: Sat Aug 29 2009 - 09:59:23 CDT

do you mean how to create a structure with min/max projection? there really
is no such thing as minimal or maximal projections along a PCA vector, the
amplitude is arbitrary. or do you mean you want to determine which
structures in the trajectory have min/max projection and extract those?

On Sat, Aug 29, 2009 at 10:43 AM, Chunliyan <>wrote:

> Dear all,
> We can use DynDom if you have two conformations of the same
> protein. These may be two X-ray structures, or structures generated using
> simulation techniques such as molecular dynamics or normal mode analysis. I
> want to ask how to get structures from principle component analysis of MD
> trajectory, and then use them to do DynDom analysis. These structures are
> the structure with the minimal projections or maximal projections for every
> modes? Is it right? If not, how we can get it. Thanks for your help.
> All the best,
> Chunli Yan
> UT at Austin
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