AMBER: hbond analysis in ptaj/carnal

From: Jana Precechtelova <>
Date: Thu, 26 May 2005 18:25:20 +0200 (MEST)

Dear Amber users,

I would like to carry out a hydrogen boding
analysis for a simple DNA d(CGCGAATTCGCG)2
in order to find out how many hydrogen bonds
are created between water and phosphate
oxygens O1P/O2P and in order to get a statistics
like: e.g.

over 10% of the trajectory, there are 3 H-bonds
to O1P and 2 H-bonds to O2P (the 3/2 configuration)

I would like to use the O1P/O2P...H(wat) distance
and O1P/O2P...H-O(wat) angle to restrict the
search for H-bonds.

1. The distance cutoff in Amber is defined with
the help of the heavy atoms distance, not
with the H-bond distance.

2. The angle definition in Amber doesn't correspond
to the standard H-bond angle definition.
In ptraj/carnal, the angle is defined as H-DONOR-ACCEPTOR. However, the
standard definition

In other words, neither the distance nor the
angle definition in Amber allows me to employ
the geometry restrictions for H-bonds that I want.

1. Is there any way in Amber how to get
a hydrogen bonding statistics using the
the H-bond distance and the DONOR-H-ACCEPTOR
angle as geometry criteria for hydrogen bonding?

2. If there is no way haw to treat the
problems 1 and 2 at the same time, is it at least
possible to overcome one of the two problems?

3. I am not sure about the definitions od the
DONOR and ACCEPTOR in ptraj and carnal.
In ptraj, DONOR seemes to be defined as a lone pair
donor, while in carnal DONOR seems to be
defined as a donor of the hydrogen atom.
It would mean that a DONOR in ptraj is
actually an ACCEPTOR i carnal and vice versa,
am I right?

Many thanks for your suggestions


         Jana Precechtelova (Ph.D. student)
         Institut fuer Anorganische Chemie
         Bayerische Julius-Maximilians Universitaet Wuerzburg
         Am Hubland, 97074 Wuerzburg, Germany
         NMR Laboratory
         National Centre for Biomolecular Research (NCBR)
         Faculty of Science, Masaryk University
         Kotlarska 2, 611 37 Brno, Czech Republic

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Received on Thu May 26 2005 - 17:53:00 PDT
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