VMD-L Mailing List

From: Sahu, Subin (sahus_at_oregonstate.edu)
Date: Thu Apr 28 2016 - 07:15:32 CDT

I found the cause of the difference. Actually I was only counting H-bonds
of the atom as a donor in 'hbond measure" and both donor and acceptor in
'hbonds' package.

Best,
Subin

On Wed, Apr 27, 2016 at 12:05 PM, Sahu, Subin <sahus_at_oregonstate.edu> wrote:

> Dear VMD users,
>
> I'm trying to find number of Hydrogen bonds for a particular oxygen atom
> in my system and I found that "hbonds" package and "measure hbonds" gives
> a very different results. The "measure hbonds" gives smaller value compare
> to the "hbonds". Could anyone help me understand why is it so? I will
> really appreciate your help.
>
> Best,
> Subin
>
> # using hbonds package
> mol load psf cons.psf dcd cons.dcd
> set sel1 [atomselect top "index 487"]
> set sel2 [atomselect top "name OH2 and not index 487"]
> package require hbonds
> hbonds -sel1 $sel1 -sel2 $sel2 -dist 3.6 -ang 30 -outfile hbondsWW.dat
>
> #using measure hbonds
> set nframes [molinfo top get numframes]
> for {set f 0} {$f<$nframes} {incr f} {
> molinfo top set frame $f
> set sel1 [atomselect top "index 487"]
> set sel2 [atomselect top "name OH2 and not index 487"]
> set hb [measure hbonds 3.6 30 $sel1 $sel2]
> set acc [lindex $hb 0]
> set n [llength $acc]
> puts $outFile "$f \t $n"
> }
> mol delete top
>