[gmx-users] Angle definition in g_hbond ...

[Mark Abraham]

sharada wrote:
> dear gmx-users,
> 
> I have a very fundamental query. I am trying to obtain the backbone 
> hydrogen bonds formed during a 15ns simulation of a 35 long protein. 
> When I do this by using g_hbond and selecting the Backbone groups, I am 
> getting no hydrogen bonds at all . However, when I plot the hydrogen 
> bonds for some of the structures picked up through the dynamics  using 
> InsightII  I am able to see the backbone  HBs in almost all of them.
> 
> This is the command I am using:
> 
>  g_hbond -f  HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num 
> hnum.xvg -g hb.log
> 
> this is the output I obtain and the hb.log file is not created :
> 
> Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision)
> Specify 2 groups to analyze:
> Group     0 (     Protein) has   358 elements
> Group     1 (   Protein-H) has   271 elements
> Group     2 (     C-alpha) has    36 elements
> Group     3 (    Backbone) has   108 elements
> Group     4 (   MainChain) has   144 elements
> Group     5 (MainChain+Cb) has   177 elements
> Group     6 ( MainChain+H) has   181 elements
> Group     7 (   SideChain) has   177 elements
> Group     8 ( SideChain-H) has   126 elements
> Group     9 ( Prot-Masses) has   358 elements
> Select a group: 3
> Selected 4: 'Backbone'
> Select a group: 3
> Selected 4: 'Backbone'
> Calculating hydrogen bonds in Backbone (108 atoms)
> Found 0 donors and 72 acceptors
> No Donors found

I haven't used this tool, but the problem looks like it is here. Are 
there any hydrogens in this group?

Mark