[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:
> 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?
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users