Gianluca Interlandi wrote:
Dear David,
Thanks for your reply,
The hbond program is rather complex, but the hbond criterion itself is not
(but note that the definition of the angle has changed from 3.2.1 to 3.3, from
AHD to ADH).
This hasn't been clear to me as the online documentation says DHA:
-a real 30 Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
in that case you're running an old version of gromacs. Try
which g_hbond
Maybe you should start by removing the options:
-nonitacc -hbm -hbn -nomerge
Do these options influence the way hydrogen bonds are calculated?
I want to know which hydrogen bond is formed in each frame. For this
reason I need "-hbm" which gives me a matrix. However, in order to know
what atoms correspond to the index in the y-axis of the matrix "hbmap.xpm"
I need "-hbn". Finally, I also need "-nomerge" because the index file
"hbond.ndx" inlcudes even those hydrogen bonds which are merged, and thus
the number of hbonds in "hbond.ndx" would not correspond to the number of
hbonds in "hbmap.xpm". But maybe there is an easier way to do this.
That's fine but I am more concerned to make sure that what is computed
is correct. It does seem to be a version problem however.
Thanks,
Gianluca
-----------------------------------------------------
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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