Re: AMBER: carnal - water-mediated HBond

From: Jiri Sponer <>
Date: Sun, 23 Jan 2005 15:52:55 +0100 (MET)

I think they mean water-bridged H-bonds.

One need to analyze explicit hydration; i.e.,
monitor exact positions of individual water molecules
with respect to solute.
Most water bridges will have enhanced water binding
residency times and close-to 100% occupancies (in a given
These interactions are quite variable and may range
from waters that are bound (DNA and RNA) for around 500ps up
to waters bound permanently on a scale of 20+ ns simulations.
May involve two (plain w-bridges), three or even four
solute atoms (pockets) and (simultaneously) more than one water molecule.
The water molecules may have a rather rigid orientation as well
as there are hydration pockets with "swinging" waters.

I think there is no way to identify water bridges based
solely on solute-solute atom distances.

Reblova et al. Long-residency hydration, cation binding and dynamics
of Loop E/Helix IV rRNA - L25 protein complex. Biophys. J. 87, 2004, 3397-3412

Spackova et al. Molecular dynamics simulations and
thermodynamics analysis of DNA - drug complexes.
Minor groove binding between 4',6-diamidino-2-phenylindole (DAPI)
and DNA duplexes in solution.
Journal of the American Chemical Society 125, 2003, 1759-1769.

best wishes Jiri

Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133
Senior Editor - Journal of Biomolecular Structure and Dynamics,
Adenine Press, NY
Senior Wellcome Trust International Research Fellow for Biomedical Science

> I have a question on calculating hydrogen bonds using carnal.
> > Is there any way to get the list of all possible HBs including the
> > water-mediated ones?
> What does water-mediated mean? From the manual:
> 'hbid' is an id from FILES_OUT, above.
> DONOR and ACCEPTOR indicate group ids for searching for the appropriate
> atoms (note: donor is the heavy atom to which the hydrogen is attached).
> **The default for either is all atoms.**
> Looking back up at FILES_OUT / HBOND:
> HBOND hbid base_file [TABLE] [LIST];
> TABLE Output table of occupancies in This table has two
> sections. The first part is a key that lists the possible hbonds in
> order. The format is:
> # 1 (ADE 2 O5' )--(HB 1 H ) .. (ADE 2 O1' )
> # 2 (ADE 2 O5' )--(HB 1 H ) .. (ADE 2 N7 )
> The second part consists of a matrix of 0's and 1's. Each column is for
> a given hbond pair according to the numbering in the key section, and
> each row (line) is for a coordinate set. The format is '0' if no hbond
> is happening, '1' if it is.
> Bill
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Received on Sun Jan 23 2005 - 15:53:00 PST
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