AMBER Archive (2006)

Subject: AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?

From: a a (
Date: Mon Aug 14 2006 - 06:25:31 CDT

Dear Sir/Madam,

I am trying to test the flexibility of a loop in a protein, after doing the
MD stimulation, I got .mdcrd file, and I could like to follow Tutorial 2
section 6 to calculate the rmsd for the 20 residues in the loop.

In tutorial 2 section 6, there is a line as follow in the
combine_mdcrds_and_strip.ptraj file:

rms first out a-dna_0-1820ps.rmsfit @P,O3',O5',C3',C4',C5' time 0.50

If I don't want to type in every atoms name after @, can I use Residue
number instead, if yes, could you mind to teach me how to do so?

Best regards,


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