[gmx-users] g_hbond -sel

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 16 17:23:10 CET 2005

Jozef Hritz wrote:
> Hi,
> I visualized my MD in VMD and I see there very often formation of hydrogen
> bond between N-H group of Trp (donor) and OB-H of FMNO (acceptor)
> However when I put the atom numbers of N H OB    into selected.ndx
> starting with [ selected ]
> and try ti find when this H-bond exists by g_hbond  with options -sel -num
> it always gives me 0 for all times. I tried also to increase -a -r 
> but nothing changed. It looks like it does not accept atom OB of FMN as
> possible hydrogen bond acceptor. On the other hand with -sel option it
> should not care about atom types.
> Can You write me if I am making something wrong, or is it known bug?
the latter.

> Thanks
> Jozef 
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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://xray.bmc.uu.se/~spoel

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