AMBER: Distance diagnolization matrix plot

From: Siddharth Rastogi <>
Date: Wed, 9 Jul 2008 12:34:08 +0530

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.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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Sun Jul 13 2008 - 06:07:03 PDT
Custom Search