[gmx-users] GMX hbond

[Dhumal, Nilesh]

Hello Gromacs users,


I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 5.1.4. I did following steps

mx hbond -f traj.trr -s md.tpr -n index.ndx -ac

Reading file md.tpr, VERSION 5.1.4 (single precision)
Specify 2 groups to analyze:
Group     0 (         System) has  2560 elements
Group     1 (          Other) has  2432 elements
Group     2 (            EMI) has  2432 elements
Group     3 (             CL) has   128 elements
Group     4 (            Ion) has   128 elements
Group     5 (            EMI) has  2432 elements
Group     6 (             CL) has   128 elements
Group     7 (              C) has   128 elements
Group     8 (             C2) has   128 elements
Group     9 (             C4) has   128 elements
Group    10 (             H9) has   128 elements
Group    11 (            H10) has   128 elements
Group    12 (            H11) has   128 elements
Group    13 (             CL) has   128 elements
Group    14 (             ch) has   256 elements
Group    15 (             ch) has     3 elements
Group    16 (             O1) has     2 elements
Select a group: 14
Selected 14: 'ch'
Select a group: 13
Selected 13: 'CL'
Checking for overlap in atoms between ch and CL
Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
Found 0 donors and 0 acceptors
Making hbmap structure...done.
No Donors or Acceptors found

-------------------------------------------------------
Program gmx hbond, VERSION 5.1.4
Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l                                                                                                              ine: 3984

Fatal error:
Nothing to be done
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Group 14 is list of donor hydrogen (eg. 4(donor)     11(hydrogen)) and group is list of acceptors . Why donors and acceptors are zero.


Thanks,
Nilesh