VMD-L Mailing List

From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Thu Feb 21 2008 - 19:06:14 CST

Hi,

I wanted to monitor the helicity change of a protein during
simulations and write a script as the following:

mol new pro.psf
animate read dcd pro.dcd beg 0 end -1 skip 10 waitfor -1

set outfile [open helicity.dat w]

set sel [atomselect top "protein and name CA"]

animate goto start
set nf [molinfo top get numframes]
for {set i 0 } {$i < $nf } { incr i } {
        animate goto $i
        mol ssrecalc top
        set helicity [$sel get structure]
        puts $outfile "$helicity"
}

close $outfile

But in the output file, the secondary structures for all the frames
are the same although they are different when I checked them in tcl
console.

Can anyone tell me why $helicity does not get updated in the loop?

Many thanks,
Jufang

------------------------------
Jufang Shan
Postdoctoral Associate
Department of Physiology & Biophysics
Weill Medical College of Cornell University
New York, NY 10065