[gmx-users] H-bond calculation

RJ rajiv at kaist.ac.kr
Wed Sep 16 08:39:37 CEST 2015

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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