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