AMBER Archive (2009)

Subject: [AMBER] Best rms fit for correlation and covariance analysis

From: Cihan Aydin (
Date: Tue Apr 28 2009 - 00:02:14 CDT

Greetings everyone,

I was wondering the best way to do an RMS fit on all MD trajectories to
obtain correlation and covariance matrices to remove the rotational and
translational degrees of freedom to the best extent. My simulations
include a two domain complex which is connected by a flexible linker
region and non-bonded contacts. I want to analyze the effect of these
non-bonded contacts through the analysis of inter-domain correlations
and projection of quasi harmonic modes on a variety of stuff...

I was thinking about using these structures for reference...

- Minimized pre-equilibrated structure
- Water & ion equilibrated structure @ 300K (the last snapshot before MD
- Average structure calculated using the whole MD trajectory

And these alignments

- All CA's
- CA's in structured core subdomains in either domain of the complex
- Selected residues with the lowest B-values
- Selected residues from double-difference plots

I tried combining some of these and obtained different results and quite
confused on which way to go... If you can provide me any insight I will
be grateful. If you provide me a better way than I thought, I will be
more grateful.


Cihan Aydin

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