VMD-L Mailing List

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Mon Dec 17 2007 - 14:52:39 CST

Dear users,
i am trying to find out if i have h-bond between two selected atoms. For
this i am using this script (below) but not getting any values, no matter
what the cutoff and angle values are...
Please help
Thank you
..............................
set outfile [open hbond.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "index 1411" frame 0]
# rmsd calculation loop
for { set i 0 } { $i <= $nf } { incr i } {
set sel [atomselect top "index 3893" frame $i]
puts $outfile "[measure hbonds 3.5 30 $sel $frame0]"
}
close $outfile