On 4/10/18 6:49 PM, Dhumal, Nilesh wrote:
I defined donor and hydrogen both in donor group. Acceptors are in acceptor 
group.

The code does not find valid donors and acceptors. Donors are NH and OH, acceptors are N and O. You'd have to modify the code to get anything else to work.

-Justin

Nilesh
________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, April 10, 2018 6:45:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:
I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 
version and used g_hbond successfully.  Could not find out why its not working 
using gmx hbond.
No version of GROMACS should have ever worked with such index groups.

A hydrogen bond must be defined by at least three atoms, because it is
based on both the D-A distance and the D-H-A angle. One cannot do the
analysis on a group that contains only H atoms. Your donors have to
include both D and H atoms, and the acceptor group the A atoms.

-Justin

Nilesh

________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond



On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
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.
Have you tried Googling the error? The first result has the answer...

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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