Dear Amber users,
OBJECTIVE:
==========
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.
PROBLEMS:
=========
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
is DONOR-H-ACCEPTOR.
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.
QUESTIONS:
==========
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
Regards,
Jana
=============================================================
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
=============================================================
email: janap.ncbr.chemi.muni.cz
=============================================================
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Received on Thu May 26 2005 - 17:53:00 PDT
