[gmx-users] implementation of hydrogen-bonding calculation

[Daan van Aalten]

further on H-bonds

Another possibility to consider is the HB2 algorithm that is used in WHAT
IF, and is described in:

Hooft, R. W. W. and Sander, C. and Vriend, G.
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein
structures
Proteins (1996) 363-376

This looks at all the distances/angles involved (not just D-A and DHA)
but more interestingly, encodes the measured properties in a "hydrogen
bond" score between 0 and 1. This is exceptionally useful especially when
looking at a range of different inhitors in complex with a protein
(of course PRODRG writes out a WHAT IF topology as well which you can use
for this) - and vastly better than things like HBPLUS.

cheers

Daan





On 5 Dec 2003, David van der Spoel wrote:

> On Fri, 2003-12-05 at 09:21, Marc Baaden wrote:
> > Hi David,
> >
> > >>> David said:
> >  >> > 	In the Gromacs mannual, the criteria for hydrogen-bonding is
> >  >> > 	1. donor-acceptor distance < 3.5 \AA and
> >  >> > 	2. acceptor-donor-hydrogen angle < 60 degree
> >  >> [..]
> >  >> This has been fixed in the next release. Now we can reproduce hbonding
> >  >> studies from the literature. We hope to put out a 3.2.0 beta version in
> >  >> the weekend and a final one before christmas.
> >
> > this is interesting. Can you comment a bit more on this ? How should
> > one do a proper h-bond analysis with gmx 3.1.4 ? Or asking the other
> > way round how useful are current g_hbond results (standard parameters) ?
> >
> It depends what you compare to. Our first implementation was meant to be
> roughly comparable to DSSP. I do not recall why we used the H-A distance
> rather than D-A, although I vaguely recall that it is used elsewhere
> too. In the new version it is an option, with D-A being the default.
>
> When I quite recently tried to reproduce literature results of water
> simulation and found some oddities, I looked into all this stuff. The
> number of hbonds can now be reproduced exactly compared to literature
> values. But there is more... In the "old" g_hbond, hbonds with multiple
> possible hydrogens connecting D and A (e.g. for water-water there are
> four Hs that can make a hbond between a given D and A) are treated as
> different hbonds. This is also contrary to what's used in the
> literature, and it now is an option to define these as separate or merge
> them to one hbond. This merging does not affect the number of hbonds,
> but is does affect the hbond autocorrelation function.
>
> Finally I built in a feature to use g_hbond for contact analysis, not
> looking at hbonds, but just atom-atom contacts within two groups
> (including contact autocorrelation).
>
> > Thanks,
> > MArc
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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