VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Aug 29 2006 - 18:15:56 CDT

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.

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.

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.
> 

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