I have a jiffy script for just that here:
http://bl831.als.lbl.gov/~jamesh/pickup/rmsd
you run it like this:
./rmsd model1.pdb model2.pdb
output looks like this:
1156 atom pairs found
RMSD(CA )= 0.516368 (129 CA pairs)
RMSD(all)= 0.506422 (1156 atom pairs)
RMSD(Bfac)= 0.489973
MAXD(all)= 1.23212 for N PRO 79
MAXD(Bfac)= 1.69 for CA GLY 102
Doesn't need a special version of awk, but you may have to edit the top
line to reflect where "awk" is on your computer. Sometimes its in
/bin/awk, or /usr/bin/awk, or (for some reason) /usr/share/awk
-James Holton
MAD Scientist
On 6/19/2012 8:04 AM, 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 (cmn...@ibmb.csic.es <mailto:cmn...@ibmb.csic.es>)
Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
Barcelona, Spain
