AMBER Archive (2009)

Subject: [AMBER] Dyndom

From: Chunliyan (chunliyan_at_mail.utexas.edu)
Date: Sat Aug 29 2009 - 09:43:00 CDT

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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