AMBER Archive (2008)

Subject: AMBER: matrxi dist command

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Apr 22 2008 - 06:37:50 CDT

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.

Regards
Priya

       
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