AMBER: matrxi dist command

From: priya priya <>
Date: Tue, 22 Apr 2008 12:37:50 +0100 (BST)

Dear All

I am trying to compute distance matrix, by selecting byatom options.
command used is
 matrix dist .CA out distmat.dat
as far as i understand it is making a matrix for the CA atoms in all the residues.

But i want to compute the matrix for side chain carbon, i.e .CB, for that I am using command:

matrix dist out distmat.dat .C = & !.CA,C

But i am not sure that it compute matrix for all carbons except backbone alpha and carbonyl carbons as it says:

PTRAJ: matrix dist out distmatC.dat .C = & !.CA,C
Mask [.C] represents 78 atoms
WARNING: Error in mask string, no "." or ":" present (=)

Or i should just use command
matrix dist .CB out distmat.dat

Please suggest me if i am doing some mistake.


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Received on Wed Apr 23 2008 - 06:07:49 PDT
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