VMD-L Mailing List

From: Aurelie.DeLuca_at_sanofi-aventis.com
Date: Fri Apr 18 2008 - 08:08:39 CDT

Hy everybody,
 
I want to do a script what calcul RMSD between two structures what they
haven't the same number of atoms. I can do it if structures have the
same number with a VMD script as following :
 
set out [open
"/global/home/i0028932/plos//CROSSED_RMSD/crossed_rmsd.dat" a]

mol delete all

mol load pdb file1.pdb

set sel0 [atomselect 0 "backbone"]

mol load pdb file2.pdb

set sel1 [atomselect 1 "backbone"]

set rmsd [measure rmsd $sel0 $sel1]

set rmsd [format "%-10.5f" $rmsd]

puts $rmsd

puts $out "1 $rmsd PAK1_DFGsemiout.pdb"

close $out

mol delete all

 

Thanks for your help.

Aurelie