AMBER Archive (2009)

Subject: RE: [AMBER] DCCM

From: Duggan, Brendan M. (bmduggan_at_musc.edu)
Date: Wed Jul 15 2009 - 11:06:57 CDT

Your ptraj command produces a data matrix which I believe is a Dynamic Cross Correlation Map. I use gnuplot to display these matrices. Gnuplot is included in most linux distributions. The following set of gnuplot commands should plot your data

set view 0,0,1,1
set pm3d map
set cbrange [-1:1]
set palette defined (0 0 0 0, 1 0 0 1, 3 0 1 0, 4 1 0 0, 6 1 1 1)
splot "ABC_corr.dat" matrix

Note that a google search for "Dynamic Cross Correlation Map" came up with this link
http://mccammon.ucsd.edu/~bgrant/bio3d/html/dccm.html
which suggests that the R package Bio3D can also plot this type of data.

brendan

email: bmduggan_at_musc.edu
phone: (843) 792 5029
fax: (843) 792 4322

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Raja Pandian [chemistryraj_at_gmail.com]
Sent: Tuesday, July 07, 2009 7:05 AM
To: AMBER Mailing List
Subject: [AMBER] DCCM

Dear Amber user,

I would like to do the Dynamic Cross Correlation Map (DCCM) analysis.
Searching AMBER archive showed that similar questions have been posted
before but no answer.

I have a question about the cross-correlation calculation using ptraj (Amber
9). I use the following input for ptraj:

matrix correl name ABC_corr @CA out ABC_corr.dat

My questions are;

1) Does the "correl" result give me the so-called "DCCM"? I noticed some
publications showed the across-correlation map that was obtained form ptraj,
it seems to me they never use the term DCCM.

2) How can I plot the correlation matrix map (ABC_corr.dat)? Could you
please suggest me a graphic program for the correlation matrix data plot?

Thanks in advance for your suggestions.

Faithfully

Rajapandian. V
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