just do this one-liner (assuming that your numbering is not messed up
and you have "the first atom")

grep 'ATOM      1' model1.pdb model2.pdb | cut -d: -f 2 | cut -c 31-54 |
awk '{printf "%s ",$0;}' | awk '{print sqrt(($1-$4)^2+($2-$5)^2
+($3-$6)^2);}'

On Tue, 2012-06-19 at 15:04 +0000, Claudia Millán Nebot wrote:

Hello everyone :)

I would like to know if it exist some tool that allows to calculate

RMSD between 2 pdbs that are identic, but just displaced in space. It

should not make a superposition, beause if this is the case it will

just say that RMSD is 0 .

I know is not such a difficult problem in terms of scripting, but i

was wondering if there are tools already.

Claudia Millán ([log in to unmask])

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs