VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 29 2006 - 17:42:56 CDT

On 8/29/06, Nitin Bhardwaj <nbhardwaj_at_gmail.com> wrote:
> Dear VMD users,
>
> I was wondering if there is a quick way to count the number of
> hydrogen bonds between a lipid molecule and a protein chain directly
> from the dcd file. I also want to use different paprameters for
> H-bonds (60 degrees as angle and 3.5 Ang as the distance cut-off).

you will need a .psf file or equivalent to be able to identify the atoms
via their names and thus locate the hydrogen bond donors and acceptors
and hydrogens. a dcd file does not contain that kind of information, only
coordinates (or velocities, or...).

once you have that figured out, you can use a code like the following:

set mol [molinfo top]
set lip [atomselect $mol "<add here selection text to identify the lipid>"]
set pep [atomselect $mol "<add here selection to identify the protein chain>"]

set nhb [llength [lindex [measure hbonds 3.6 60 $lip $pep] 0]]
puts "number of h-bonds: $nhb"

if you want this for the whole trajectory, you just add a loop
of the the frames to this:

set nf [molinfo $mol get numframes]
for {set i 0} {$i < $nf} {incr i} {
  $lip frame $i
  $pep frame $i
  set nhb [llength [lindex [measure hbonds 3.6 60 $lip $pep] 0]]
  puts "number of h-bonds in frame $i: $nhb"
}

similar stuff should be in the mailing list archives.

cheers,
    axel.

>
> thanks a lot in advance.
> Rgds,
> Nitin
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.