AMBER: across-correlation in ptraj

From: Xin Hu <>
Date: Wed, 2 Mar 2005 11:20:09 -0500

Dear Amber user,
I have a question about the across-correlation calculation using ptraj (Amber 8). I use the following input for ptraj:

trajin ABC.mdcrd
reference ABC_mdaverge.pdb
rms reference .CA
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?

I apprecaited very much for your help!


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Received on Wed Mar 02 2005 - 16:53:02 PST
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