[gmx-users] H-bond calculation

[RJ]

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.