# Duplicate atom index (1) in virtual\_sites3 error when running command "gmx grompp -f ions.mdp " **URL:** \ **Category:** User discussions\ **Tags:** grompp, mdrun\ **Created:** [July 26, 2021, 9:24am UTC](https://gromacs.bioexcel.eu/t/duplicate-atom-index-1-in-virtual-sites3-error-when-running-command-gmx-grompp-f-ions-mdp/2596 "2021-07-26T09:24:35Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![rijja](https://avatars.discourse-cdn.com/v4/letter/r/4491bb/32.png) [@rijja](https://gromacs.bioexcel.eu/u/rijja)\ **Post date:** [July 26, 2021, 9:24am UTC](https://gromacs.bioexcel.eu/t/duplicate-atom-index-1-in-virtual-sites3-error-when-running-command-gmx-grompp-f-ions-mdp/2596/1 "2021-07-26T09:24:35Z")
GROMACS version: 2019.6 GROMACS modification: No Here post your question I am running the command “gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr” I am getting the following error ““Fatal error: There was 1 error in input file(s)”” because of this error " ERROR 1 [file inhib1.itp, line 81]: Duplicate atom index (1) in virtual\_sites3 " in my itp file: [virtual\_sites3] ; Site from funct a d 10 5 1 1 2 0 -0.220 [exclusions] ; ai aj 5 10 1 10 1 1 10 2 1 10 6 1 10 7 1 10 3 1 10 4 1 I am using charmm36-feb2021.ff for protein topology and CGenFF version 4.4 for ligand toplogy.unable to understand why still getting this error. kindly guide. Regards, Rijja ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 26, 2021, 12:27pm UTC](https://gromacs.bioexcel.eu/t/duplicate-atom-index-1-in-virtual-sites3-error-when-running-command-gmx-grompp-f-ions-mdp/2596/2 "2021-07-26T12:27:38Z")
You’re using a very old version of the script, one that exploited a hack in version 2016 that allowed for duplicate atom indices. Use a newer version of the script from the MacKerell lab website and make sure you’re using the latest GROMACS version to make use of a new type of virtual site construction that halogens require in CGenFF. ---
**Author:** ![rijja](https://avatars.discourse-cdn.com/v4/letter/r/4491bb/32.png) [@rijja](https://gromacs.bioexcel.eu/u/rijja)\ **Post date:** [July 27, 2021, 4:55am UTC](https://gromacs.bioexcel.eu/t/duplicate-atom-index-1-in-virtual-sites3-error-when-running-command-gmx-grompp-f-ions-mdp/2596/3 "2021-07-27T04:55:17Z")
Hi Jalemkul,thank you for your quick reply. I am using the feb2021 version of both charmm36 and CGenff.I am using py2 script of cgenff\_charmm2gmx.py. Should I use py3, is that the issue? For gromacs I am using the 2019.6 version. All are latest except gromacs which is also 2019, which I think does not have the hack. Kindly guide, Grateful, Rijja ---
**Author:** ![harunalcakan](https://avatars.discourse-cdn.com/v4/letter/h/df705f/32.png) [@harunalcakan](https://gromacs.bioexcel.eu/u/harunalcakan)\ **Post date:** [December 26, 2023, 12:20pm UTC](https://gromacs.bioexcel.eu/t/duplicate-atom-index-1-in-virtual-sites3-error-when-running-command-gmx-grompp-f-ions-mdp/2596/4 "2023-12-26T12:20:05Z")
Hello, have you figured out this issue?