VMD-L Mailing List

From: Monika Sharma (mon_sharma_at_research.iiit.ac.in)
Date: Mon Mar 02 2009 - 01:18:30 CST

Dear All,
I am trying to calculate the RMSD of a nucleic acid trajectory "nuc.dcd"
with reference of pdb "nuc-ref.pdb". When I am loading the tcl file for
computation, there is some problem with the computation and the output file
is showing no output written.
I am writing on vmd text terminal as:
> vmd -dispdev text -dcd nuc.dcd -psf nuc.psf
....DCD gets loaded...
vmd> mol load pdb nuc-ref.pdb
.. PDB gets loaded..
vmd> source rmsd-time.tcl

tcl file read as:
proc print_rmsd_through_time {{mol top}} {
        set outfile [open rmsd-compare-merge.dat w]
          # the reference frame
        set reference [atomselect 1 "nucleic and noh"]

        set compare [atomselect $mol "nucleic and noh"]

        set num_steps [molinfo $mol get numframes]
        for {set frame 0} {$frame < $num_steps} {incr frame}
      {
                   $compare frame $frame
             # compute the transformation
         set trans_mat [measure fit $compare $reference]
             # do the alignment
             $compare move $trans_mat
             # compute the RMSD
         set rmsd [measure rmsd $compare $reference]
           # print the RMSD
       puts $outfile "$frame $rmsd"

       }
 }
vmd> print_rmsd_through_time

The commands do execute but nothing is written in the output file.
Any suggestion are welcome.

Thanks in advance

Regards
Monika Sharma