Re: About calculating RMSD with rmsd.tcl

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Oct 05 2005 - 22:22:23 CDT

Boyang,
how many frames do you have in your trajectory? And do you see this
change happen in the first frame, or one of the subsequent frames?
Peter

Boyang Wang wrote:

> 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!
> Boyang
>
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