VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Mar 02 2009 - 01:42:38 CST

Dear Monika,

On Mon, Mar 2, 2009 at 1:18 AM, Monika Sharma
<mon_sharma_at_research.iiit.ac.in> wrote:
> 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.

You need to close the file you're writing to:
close $outfile

Also, make sure your trajectory is the top molecule or call
'print_rmsd_through_time 0'.

Cheers,
Leo

>
> Thanks in advance
>
> Regards
> Monika Sharma
> 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign