[gmx-users] Hydrogen bonds with version 3.3.1

David van der Spoel spoel at xray.bmc.uu.se
Tue May 2 09:05:05 CEST 2006

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 gianluca at u.washington.edu
>                     +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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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