About calculating RMSD with rmsd.tcl

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Fri Sep 30 2005 - 19:55:26 CDT

Hi all. I am calculating the rmsd of a peptide ALA-ALA-LYS. Here is the .tcl file I am using:
set outfile [open rmsd.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top "resname ALA LYS" frame 0]
set sel [atomselect top "resname ALA LYS "]
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
    $sel frame $i
    $sel move [measure fit $sel $frame0]
    puts $outfile "[measure rmsd $sel $frame0]"
close $outfile

I put "resname ALA LYS" in the script because I think this is a way to include the whole protein. I also tried to replace the "resname ALA LYS" by "protein".
Now I have a problem. After I type in "source rmsd.tcl" in the TKconsole interface, vmd finishes the calculation, but I have found that the position of the peptide has suddenly shifted a little bit (~0.2 Angstrom), and I see this shift in the calculated rmsd.dat. Just to repeat, this "shift" happens exactly when I hit "enter" after I typed in "source rmsd.tcl".
I don't know what is wrong and would like to hear from you guys.
Thanks for your time!


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