From: Michel Espinoza-Fonseca (
Date: Wed Nov 30 2005 - 06:34:26 CST

Dear all,
I've been trying to calculate the presence or absence of a specific hbond within my trajectory. Unfortunately, I haven't succeeded. I'm using the following script, but is not working:
set outfile [open hbonds.txt w]
set nf [molinfo top get numframes]
set D [atomselect top "resid 54"]
set A [atomselect top "resid 23"]
for {set i 0} {$i<$nf} {incr i} {
set hbonds [measure hbonds 3.0 25 $D $A]
puts $outfile "Frame $i, $hbonds"
close $outfile
When I run my script, I get that this hbond exist in all frames! And when I visualize the same frames on VMD, they don't exist. I would like to know if any of you have any idea, or if I'm skipping something important to successfully get the presence of hbonds (for sure I'm missing something!)
Thanks a lot