[gmx-users] g_hbond -sel

Jozef Hritz hritz at seneca.science.upjs.sk
Fri Dec 16 15:26:02 CET 2005


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?


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