package require psfgen
package require pbctools    

set topol "DNA_WAT.top"  
set output "water_3.5A.dat"         
set OUT [open $output "w"]   

set j 0                   
set f [open "crd.in" ]
while {[gets $f line] } {           
mol load parm7 $topol                 
mol addfile $line type crdbox waitfor all       
set framnr [molinfo top get numframes]          
puts "$framnr"                                  

molinfo top set a 66                              
molinfo top set b 67
molinfo top set c 63                            

set sel1 "all"                                  
set sel2 "nucleic"                               

pbc unwrap -sel $sel2 -all                      
pbc wrap -sel $sel1 -center $sel2 -all         

set sel3 "nucleic and (resid 291 to 298 303 to 310 and (name N3 N7 O6 O2 04 O1P O2P))"                  

set cutoff 3.5
set all [atomselect top "all"]

for {set frame 0} {$frame <= $framnr-1} {incr frame} {

animate goto $frame
display update


set j [expr $j + 1]
set moleculebin [atomselect top "(water and name O) and within $cutoff of ($sel3)"]
set check [lsort -unique [$moleculebin get resid]]
set i 0
foreach resid $check {
set i [expr $i + 1]
}
puts $OUT "$j $i"
}
mol delete 0
}
close $f