# Group Water\_and\_ions referenced in the .mdp file was not found **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [June 18, 2022, 7:40pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321 "2022-06-18T19:40:56Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![serta](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@serta](https://gromacs.bioexcel.eu/u/serta)\ **Post date:** [June 18, 2022, 7:40pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/1 "2022-06-18T19:40:57Z")
GROMACS version: GROMACS modification: Yes/No Hello, I have got an error about water\_ions not found Firstly I have an error about NA molecules > ERROR 1 [file topol.top, line 109640]: > No such moleculetype NA > I have posted a question about it ([ERROR No such moleculetype NA](https://gromacs.bioexcel.eu/t/error-no-such-moleculetype-na/4318)) Then I have change their name from NA in topol and solv\_ion files to SOD, because when I check the ion.itp file I found this lines: > [moleculetype] > ;Sodium Ion > ; molname nrexcl > SOD 3 > so, I assume that I have to change the name of NA to SOD. > The code run correctly and other next lines but when I was in code line: I have used the line gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr I got an error: this is the whole message > ``` > :-) GROMACS - gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: > > 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 grompp, version 2020.1-Ubuntu-2020.1-1 > Executable: /usr/bin/gmx > Data prefix: /usr > Working dir: /mnt/d/Articles/Y MDs/Works/2022/Linani > Command line: > gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr > > Ignoring obsolete mdp entry ‘title’ > Ignoring obsolete mdp entry ‘ns\_type’ > Setting the LD random seed to 1848058077 > Generated 167799 of the 167910 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 117519 of the 167910 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_C’ > turning H bonds into constraints… > Excluding 3 bonded neighbours molecule type ‘cp11’ > turning H bonds into constraints… > Excluding 2 bonded neighbours molecule type ‘SOL’ > turning H bonds into constraints… > Excluding 3 bonded neighbours molecule type ‘SOD’ > turning H bonds into constraints… > Setting gen\_seed to -458316911 > Velocities were taken from a Maxwell distribution at 300 K > > * * * > > Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1 > Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2701) > > Fatal error: > Group Water\_and\_ions referenced in the .mdp file was not found in the index > file. > Group names must match either [moleculetype] names or custom index group > names, in which case you must supply an index file to the ‘-n’ option > of grompp. > > 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) How to fix this error? ---
**Author:** ![Teslim](https://avatars.discourse-cdn.com/v4/letter/t/f1d935/32.png) [@Teslim](https://gromacs.bioexcel.eu/u/Teslim)\ **Post date:** [June 19, 2022, 3:19pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/2 "2022-06-19T15:19:09Z")
Did you recreate the index file after the “SOD to NA” change? ---
**Author:** ![serta](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@serta](https://gromacs.bioexcel.eu/u/serta)\ **Post date:** [June 19, 2022, 4:20pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/3 "2022-06-19T16:20:42Z")
Dear Teslim I did not create the index file how to create it? ---
**Author:** ![Teslim](https://avatars.discourse-cdn.com/v4/letter/t/f1d935/32.png) [@Teslim](https://gromacs.bioexcel.eu/u/Teslim)\ **Post date:** [July 4, 2022, 10:17pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/4 "2022-07-04T22:17:24Z")
use the [make\_ndx](https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html) with the trajectory or coordinate file to generate the index ---
**Author:** ![Bhaskarjyaa](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/bhaskarjyaa/32/1557_2.png) [@Bhaskarjyaa](https://gromacs.bioexcel.eu/u/Bhaskarjyaa)\ **Post date:** [July 6, 2022, 10:53am UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/5 "2022-07-06T10:53:46Z")
Fatal error: Group Water\_and\_ions referenced in the .mdp file was not found in the index file. I am facing a similar error while doing the NVT step. Please help. ---
**Author:** ![ashish](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@ashish](https://gromacs.bioexcel.eu/u/ashish)\ **Post date:** [November 13, 2022, 6:27pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/6 "2022-11-13T18:27:19Z")
You need to create the index file for “Protein\_Lig” and “Ion\_Water” during equilibration stage. ---
**Author:** ![HenriqueBarros](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/henriquebarros/32/1185_2.png) [@HenriqueBarros](https://gromacs.bioexcel.eu/u/HenriqueBarros)\ **Post date:** [November 17, 2022, 2:43am UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/7 "2022-11-17T02:43:42Z")
My problem is the same. “Fatal error: Group Water\_and\_ions referenced in the .mdp file was not found in the index file.” Any sugestion other than that?? ---
**Author:** ![HenriqueBarros](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/henriquebarros/32/1185_2.png) [@HenriqueBarros](https://gromacs.bioexcel.eu/u/HenriqueBarros)\ **Post date:** [November 17, 2022, 2:47am UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/8 "2022-11-17T02:47:07Z")
Ashish, you say in the part of the command “gmx make\_ndx -f em.gro -o index.ndx”?? I need to create a file by selecting Protein\_Ligand and another Water\_ions using this command twice, am I right? Did it work for you? I’m amateur, sorry. ---
**Author:** ![DaminiMehra](https://avatars.discourse-cdn.com/v4/letter/d/7bcc69/32.png) [@DaminiMehra](https://gromacs.bioexcel.eu/u/DaminiMehra)\ **Post date:** [November 23, 2022, 11:52pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/9 "2022-11-23T23:52:19Z")
If you changed NA to SOD then you need to make a new index file to include SOD. And then replace Water\_and\_ions with SOD\_Water in the.mdp file. ---
**Author:** ![HenriqueBarros](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/henriquebarros/32/1185_2.png) [@HenriqueBarros](https://gromacs.bioexcel.eu/u/HenriqueBarros)\ **Post date:** [November 29, 2022, 11:19am UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/10 "2022-11-29T11:19:02Z")
Perfect! Thanks, really. ---
**Author:** ![sakil12](https://avatars.discourse-cdn.com/v4/letter/s/4da419/32.png) [@sakil12](https://gromacs.bioexcel.eu/u/sakil12)\ **Post date:** [September 2, 2023, 2:19pm UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/11 "2023-09-02T14:19:49Z")
![NVT_tpr_problem](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/13098ceea76cc50c5afbe40df68df2e1f62f173f.png) i am facing the same problem in NVT.tpr step ; plz help me . ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [September 3, 2023, 7:40am UTC](https://gromacs.bioexcel.eu/t/group-water-and-ions-referenced-in-the-mdp-file-was-not-found/4321/12 "2023-09-03T07:40:27Z")
You need to make sure the group is included in the index file. You should be able to use gmx make\_ndx to create the group and specify which atoms should be in the group. If you’d already made that group previously, double check the index.ndx file to make sure the group is under the same name as what is called in the mdp file.