From: Subrata Paul (
Date: Thu May 31 2012 - 10:40:13 CDT

Dear sir
I am simulating a water system in AMBER10 and want to calculate water-water
I have used followinf scrip in vmd tk console

set outfile [open numHbonds.dat w]
set numframes [molinfo top get numframes]
set cutoff 3.4
set angle 60
set sel1 [atomselect top "name O"]
set sel2 [atomselect top "name O"]
for {set i 0} {$i < $numframes} {incr i} {
$sel1 frame $i
$sel2 frame $i
puts $outfile "[measure hbonds $cutoff $angle $sel1 $sel2]"
close $outfile

Is there my selection is ok??

I have attache d the out file but do not understand the out file?

what should be scripts for hbond vs time?

with appreciate

*With Best Regards
PhD Student
Dept of Chemistry.