[gmx-users] H-bond calculation

[Erik Marklund]

Dear RJ,

I don’t remember exactly how the groups are treated internally, but I think you might need to include the hydrogen in the donor group.

Kind regards,
Erik

> On 16 Sep 2015, at 07:39, RJ <rajiv at kaist.ac.kr> wrote:
> 
> Dear gmx,
> 
> 
> I would like to calculate the H-bond occupancy between two residue (intra mol inter Thr183 (OG1) -Tyr162 (N) ).
> 
> 
> I made a .ndx file choosing the both atoms : Group    40 (      r_162_&_N) has     1 elements
>                                                                     Group    41 (    r_183_&_OG1) has     1 elements
> 
> 
> and given the " gmx hbond -f prd_noPBC.xtc -s em.tpr -n index.ndx -dist hbdist.xvg -hbn hbond.ndx -hbm hbmap.xpm -tu ns "  
> 
> 
> but they end up in error as follows: Found 0 donors and 2 acceptors
> Making hbmap structure...done.
> No Donors found.
> 
> 
> 
> 
> I wonder how can i calculate the intra molecular residue-residue hydrogen bond over time as well as their occupancy in percentage? Thanks.
> -- 
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