VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Mon Dec 17 2007 - 19:03:50 CST

Quoting Narender Singh Maan <nsmaan_at_gmail.com>:

> 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
>

If you select the H-atom, measure hbonds will not get anything - you should
select instead the heavy atom it is attached to.
The selection order is:
<donor heavy atom, to which H is covalently bonded> <acceptor>

Also, do you know whether you can measure H-bonds across different frames?
If not, use something like this:

set outfile [open hbond.dat w]
set nf [molinfo top get numframes]
set selA [atomselect top "index ****"]
set selB [atomselect top "index ****"]
# frames loop
for { set i 0 } { $i <= $nf } { incr i } {
$selA frame $i
$selB frame $i
puts $outfile "[measure hbonds 3.5 30 $selA $selB]"
}
close $outfile

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