VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Thu Nov 17 2005 - 02:50:19 CST

Hi all,
first this is my first script in tcl/vmd and I need of course feedback.
I have 100 structures and I want to calculate the rmsd in a such way:
structure_1 structure_2 rmsd
1 2 rmsd12
1 3 rmsd13
1 4 rmsd14
.......
1 100 rmsd1100
2 3 rmsd23
2 4 rmsd24
.....
and so on.
Below there is a script but it does not work properly. Could someone
help me to understand what is wrong in it. Second, to run it, do I need
to run in vmd console or can I run in a shell like vmd -script
script,without gui ?

proc calculate_rmsd {}{
for { set i 1 } { $i < 100 } { incr i } {
# pro is the root of the name of my structures
        mol load pdb pro_i.pdb
        set sel1 [atomselect "backbone"]
        for { set j i+1 } { $j < 100 } { incr j } {
                set sel2 [atomselect j "backbone"]
                set rmsd [measure rmsd $sel1 $sel2]
                puts RMSD of $i $j is $rmsd
}

Thanks

Regards,

andrea 

-- 
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Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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