[gmx-users] Hydrogen bonds with version 3.3.1

David van der Spoel spoel at xray.bmc.uu.se
Tue May 2 10:51:38 CEST 2006

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 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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