From: Miguel Ferreira (
Date: Mon Apr 16 2007 - 10:10:03 CDT


I am confused about the best way to count the number of hbonds. In the
manual it is said that “The output of hbonds cannot be considered 100%
accurate if the donor and acceptor selection share a common set of atoms”.
What does this exactly means?
I am using the following script to count the number of hbonds of a protein
during a MD.:

set outfile [open "hbond.txt" w]
set nf [molinfo top get numframes]
set sel [atomselect top "resid 1 to 576 and (name \"N.*\" \"O.*\" \"S.*\")"]
for {set i 0} {$i < $nf} {incr i} {
  $sel frame $i
  set hbond [llength [lindex [measure hbonds 3.5 60 $sel] 0]]
  puts $outfile "number of h-bonds in frame $i: $hbond"
close $outfile

Is there any way to modify this script to get the correct number of hbonds?
yes, how?


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