VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 29 2006 - 19:16:19 CDT

On 8/29/06, Nitin Bhardwaj <nbhardwaj_at_gmail.com> wrote:
> Thanks Axel for an instant and detailed explaination. I just had two
> quick questions:
>
> 1) When I use H-bonds representation for both the lipid and the
> peptide, it gives me more h-bonds for the same set of parameters than
> the script you gave me. I was wondering why is this discrepancy. For
> example I can see 2 bonds when I draw them in H-bonds rep but the
> script only gives 1 bond.

the two implementations are slightly different. it might be
that you have a borderline case.

> 2) Also I hope that the script would not count the H-bonds between the
> atoms from the lipid itself, apart from the ones between the lipid and
> peptide.

please see the user's guide about this. e.g. at:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html

one selection provides the donors and one the acceptors.
if lipid/protein can be both you have to do the measurement twice
with both selections interchanged and sum the result.

cheers,
    axel.
>
> thanks a lot again.
> Rgds,
> Nitin
>
> On 29/08/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > 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.
> >
>
>
> --
> $B&-(BI+I$B'*(B
>
> 

-- 
=======================================================================
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.