AMBER Archive (2008)

Subject: AMBER: Distance diagnolization matrix plot

From: Siddharth Rastogi (
Date: Wed Jul 09 2008 - 02:04:08 CDT

Dear AMBER Users,

I am finding difficult to make CA RMSD matrix Plot from the distance matrix
of all CA atoms.
The inputs I have in ptraj is as follows:

reference inpcrd
strip :WAT
strip :Cl-
rms reference :1-100_at_CA
center :1-100 mass origin
image origin center
matrix dist @CA out distmat.dat byres mass

Now I have the distmat.dat file, from this how to get the CA RMSD matrix ?
Can anyone help me in this regard ?

Thanks in advance

Siddharth Rastogi

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