AMBER Archive (2004)

Subject: AMBER: RMSD calculations in ptraj and Carnal

From: Joseph Nachman (
Date: Tue Jun 15 2004 - 13:24:38 CDT

Hello -

I'm performing simulated annealing on a protein-peptide complex. The
simulation is performed in vacuo, with no periodic box, using Sander
Classic in Amber6. Since I'm intersted onmly int he C-trmilan segment of
the bound peptide, I keep all the protein, as well as the N-terminal
segment of the peptide fixed, so all the resulting structures are

When I try to to measure the RMSDs of CA atoms between various structures
resulting from the simulation and the - superimposed - reference structure
I get different results when using ptraj or Carnal, and both are totally
different from the results that I get if I calculate the rmsd by hand,
using the distances CAs between the various frames and the reference
structure. So I wonder as to what's going on, and whether RMSD means the
same thing in ptraj and Carnal.

Any suggestion welcome!



I can provide samples of my input files, as well as of the coordinates I

Joseph Nachman				Department of Biochemistry		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada

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