# Generate index files for gmx angle command **URL:** \ **Category:** User discussions\ **Tags:** mdrun, analysis-tools\ **Created:** [April 3, 2023, 2:11am UTC](https://gromacs.bioexcel.eu/t/generate-index-files-for-gmx-angle-command/6091 "2023-04-03T02:11:29Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [April 3, 2023, 2:11am UTC](https://gromacs.bioexcel.eu/t/generate-index-files-for-gmx-angle-command/6091/1 "2023-04-03T02:11:29Z")
GROMACS version: 2022.2 GROMACS modification: No Here post your question Hi All, I need to create an index file containing angles using the “gmx mk\_angndx” command. “gmx mk\_angndx -s prd.tpr -n angle.ndx -type angle -hq -1” This was the command I used for that. But this gave me an empty output file. My system contains water molecules. Does anyone know the reason for the empty output file? Thank you Kalpani ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [April 3, 2023, 6:18am UTC](https://gromacs.bioexcel.eu/t/generate-index-files-for-gmx-angle-command/6091/2 "2023-04-03T06:18:52Z")
From what I understand, I don’t think mk\_angndx returns indices for water molecules (at least I couldn’t find a way to get it to do so, if someone knows how then please correct me), if you were to simulate a protein in your system, then the command should work for the atoms of that protein. You should be able to find the data on the angles of the water molecules from the .itp file of the water model you used in the folder containing your forcefield. ---
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [April 24, 2023, 2:05am UTC](https://gromacs.bioexcel.eu/t/generate-index-files-for-gmx-angle-command/6091/3 "2023-04-24T02:05:53Z")
Thank you very much.