mol new ionized.psf type psf
mol addfile ionized.pdb type pdb
mol addfile output.dcd type dcd first 0 last -1 step 30 waitfor all
set outfile [open rmsdLig.dat w];                                             
set nf [molinfo top get numframes]
set frame0 [atomselect top "resid 3941 to 3970" frame 0]
set sel [atomselect top "resid 3941 to 3970"]
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
    $sel frame $i
    $sel move [measure fit $sel $frame0]
    puts $outfile "[measure rmsd $sel $frame0]"
}
close $outfile
#calculation of RMSF of CA atom using superposition
#works when pdb and dcd files are preloaded using GUI(no psf #needed)  
set num_frames [molinfo top get numframes]
set kk [expr $num_frames - 1]
set a [atomselect top "resid 3941 to 3970"]
set c [atomselect top "resid 3941 to 3970" frame $kk]
 for {set i 0} {$i<$num_frames} {incr i} {
 $a frame $i
 $a move [measure fit $a $c]
 }
set outfile [open "rmsf_CALig.dat" "w"]
puts $outfile "Residue \t RMSF"
for {set i 0} {$i <  [$a num] } {incr i} {
	set rmsf [measure rmsf $a first 1 last $kk step 10]
  	puts $outfile "[expr {$i+1}] \t [lindex $rmsf $i]"
  }
close $outfile