Gianluca Interlandi wrote:
Dear gmx-users,
I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would
like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle
cutoff of 60 degrees. For that I'm using the following command:
g_hbond -f simulation.trr -s topol.tpr -r 0.27 -a 60 -noda -nonitacc -hbm
-hbn -nomerge
Using the -noda option makes that the distance is computed from the HA
angle, but the angle is still computed from the HDA (check the source in
low_is_hbond, file gmx_hbond.c).
Maybe you should start by removing the options:
-nonitacc -hbm -hbn -nomerge
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).
If you can reproducibly prove the problem your welcome to submit a
bugzilla, or comment to the existing one.
It seems that the cutoff "-a 60" is used on the angle
Donor-Hydrogen-Acceptor instead of Hydrogen-Donor-Acceptor. As a result it
selects hydrogen bonds which are extremely bent and disregards hydrogen
bonds which are almost planar. This is exaclty the contrary of what it
should do. Does anyone have experience in calculating hydrogen bonds with
version 3.3.1?
Thanks a lot,
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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