rmsd calculation for RNA

From: Moumita Maiti (m.moumita_at_gmail.com)
Date: Fri Jun 08 2007 - 11:48:58 CDT


                I have trajectory output "dcd" file after running NVT
equilibration for a RNA molecule. I use it to calculate rmsd using
rmsd.tcl given in manual where I replace protein by rna as I do not
find right keyword.
I have run "source rmsd.tcl" in TK console of vmd extension after loading
final psf and dcd files. But it gives parse error and do not produce output
rmsd.dat. Please let me know the right keyword to use for RNA/DNA molecule.
Here is the rmsd.tcl follows:

 set outfile [open rmsd.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "rna and backbone and noh" frame 0]
set sel [atomselect top "rna and backbone and noh"]
#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

Thanks in advance,

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