AMBER Archive (2005)

Subject: AMBER: across-correlation in ptraj

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Wed Mar 02 2005 - 10:20:09 CST

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!

Xin 

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