From: Bian Li (libian1128_at_gmail.com)
Date: Mon May 30 2011 - 22:22:48 CDT

Dear all,

I performed a 50ns simulation and tried to calculate it's RMSD by using
bigdcd

my tcl script is as follows

source bigdcd.tcl
proc myrmsd { frame } {
  global ref sel all
  $all move [measure fit $sel $ref]
  puts "$frame: [measure rmsd $sel $ref]"
}
set outfile [open d2r_rmsd.dat w]
set mol [mol addfile d2r_popcwi.pdb type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "protein and backbone and noh" frame 0]
set sel [atomselect $mol "protein and backbone and noh"]
mol addfile d2r_popcwi.pdb type pdb waitfor all
bigdcd myrmsd dcd d2r_popcwieq-04.dcd
bigdcd_wait
The problem is I can't get a *.dat file that contains the output information
of RMSD calculation. When I execute this
script in the Tk console, the output simply flushes in the Tk console window
and no written *.dat output file.

Is there anybody that encountered the same kind of problems?
Can anyone help me modify this script to get the *.dat file that contains
the output information of RMSD calculation?

Thanks!

Best regards
LI Bian