VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 03 2005 - 14:28:24 CST

Hi,
  If you're just looking for a rough count and have no specific
donor/acceptor criteria, you could loop over all frames evaluating
the count simply as I illustrate below. I added the warning message
at the front as this routine can't be trusted 100% without specifying
the donors/acceptors explicitly (as mentioned in the User's Guide).

puts "Warning: The output of hbonds cannot be considered 100% accurate if the donor and acceptor selection share a common set of atoms."
set numframes [molinfo top get numframes]
set sel [atomselect top all]
for {set i 0} {$i < $numframes} {incr i} {
  $sel frame $i
  set hbondcount [llength [lindex [measure hbonds 3.5 30 $sel] 0]]
  puts "Frame $i, $hbondcount hbonds"
}
puts "Warning: The output of hbonds cannot be considered 100% accurate if the donor and acceptor selection share a common set of atoms."

On Thu, Mar 03, 2005 at 03:33:34PM -0000, syma khalid wrote:
> Does anyone have a script that will produce number of hbonds per frame
> or some thing along those lines from the standard vmd output from
> measure hbond (for a trajectory).
>
> Thanks in advance,
>
> -Syma
>
> ***********************************************************************
>
> Dr Syma Khalid
> Lab. of Molecular Biophysics,
> Department of Biochemistry,
> University of Oxford
> South Parks Road,
> Oxford
> OX1 3QU
> U.K.
> Email syma_at_biop.ox.ac.uk
>
>
> ***************************************************
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078