# H-bond calculation **URL:** \ **Category:** User discussions\ **Tags:** gmx-hbond\ **Created:** [September 2, 2023, 7:16pm UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124 "2023-09-02T19:16:38Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![samapika](https://avatars.discourse-cdn.com/v4/letter/s/9fc348/32.png) [@samapika](https://gromacs.bioexcel.eu/u/samapika)\ **Post date:** [September 2, 2023, 7:16pm UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124/1 "2023-09-02T19:16:39Z")
GROMACS version:2020.2 GROMACS modification: No I am calculating the number of H-bond and ACF of H-bond using gmx hbond command. I have a bilayer which I have divided into bins along the z axis as: Interface region, Hydrophobic core and Far interface region. In each bin I am calculating h-bond between two groups which I have filtered using gmx select command and created their indices. This index I have used as input. I am using the following command: hbond -f …/production.xtc -s …/production.tpr -n FR1\_DMS\_water.ndx -ac FR1.xvg -b 0 -e 50 but the error displays:Fatal error: Partial overlap between groups ‘resname’ and ‘resname’ How can I resolve this?? ---
**Author:** ![samapika](https://avatars.discourse-cdn.com/v4/letter/s/9fc348/32.png) [@samapika](https://gromacs.bioexcel.eu/u/samapika)\ **Post date:** [September 3, 2023, 12:11am UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124/2 "2023-09-03T00:11:10Z")
There is no overlap between two molecules. I crosschecked the .gro file. Also the elements are differently named. Please help me understanding the error. ---
**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\ **Post date:** [September 3, 2023, 12:43pm UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124/3 "2023-09-03T12:43:05Z")
Please define **different groups** in your **index file** (\*.ndx) and make sure you’re using the latest GROMACS version, **2023.2**. Here is a discussion that might be helpful to you: > [@Hbond for docked protein-protein complex](https://gromacs.bioexcel.eu/t/hbond-for-docked-protein-protein-complex/3529): > > GROMACS version: 2020.2 GROMACS modification: No Hi, I have a docked protein-protein complex and performed md simulations. I want to make a hydrogen bond study between these 2 proteins using gmx hbond ( gmx hbond -f md.xtc -s md.tpr -num hbnum\_Pro-Pro.xvg and issuing Protein , Protein (same atom numbers for both)) however, I believe this way I’m looking at intraprotein H bonds instead of interprotein H bonds, right? The md simulation was run using a pdb file with the two protein chains in it… ---
**Author:** ![samapika](https://avatars.discourse-cdn.com/v4/letter/s/9fc348/32.png) [@samapika](https://gromacs.bioexcel.eu/u/samapika)\ **Post date:** [September 4, 2023, 9:18am UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124/4 "2023-09-04T09:18:06Z")
This is the index file. [IW] 15241 15242 15243 15261 15262 15263 15525 15526 15527 15657 15658 15659 16001 16002 16003 16049 16050 16051 16229 16230 16231 16385 16386 16387 …[IDMS] 15473 15474 15475 16233 16234 16235 16309 16310 16311 16313 16314 16315 16613 16614 16615 16797 16798 16799 17177 17178 17179 17181 17182 ~/Downloads/gromacs-2020.2/build\_new/bin/gmx hbond -f ../../production\_500ps.xtc -s ../../production\_500ps.tpr -ac hbond\_idms.xvg -b 450 -e 500 -n try.ndx :-) GROMACS - gmx hbond, 2020.2 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx hbond, version 2020.2 Executable: /home/user/Downloads/gromacs-2020.2/build\_new/bin/gmx Data prefix: /home/user/Downloads/gromacs-2020.2 (source tree) Working dir: /DATA2/DMSO+DMPC/simulation/Slipid/25%/gromacs-2020.2/new\_pack/npt/production/production\_500ps/h-bonds/generation\_of\_IW\_IDMSO Command line: gmx hbond -f ../../production\_500ps.xtc -s ../../production\_500ps.tpr -ac hbond\_idms.xvg -b 450 -e 500 -n try.ndx Reading file ../../production\_500ps.tpr, VERSION 2020.2 (single precision) Specify 2 groups to analyze: Group 0 ( IW) has 393 elements Group 1 ( IDMS) has 60 elements Select a group: 1 Selected 1: ‘IDMS’ Select a group: 0 Selected 0: ‘IW’ Checking for overlap in atoms between IDMS and IW * * * Program: gmx hbond, version 2020.2 Source file: src/gromacs/gmxana/gmx\_hbond.cpp (line 2736) Fatal error: Partial overlap between groups ‘IDMS’ and ‘IW’ ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)