# Protein-protein interaction tutorial **URL:** \ **Category:** User discussions\ **Tags:** simulation-setup\ **Created:** [April 25, 2024, 9:35am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985 "2024-04-25T09:35:35Z")\ **Posts on this page:** 9\ **Page:** 2
**Author:** ![sizhe\_Li](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sizhe\_Li](https://gromacs.bioexcel.eu/u/sizhe_Li)\ **Post date:** [December 20, 2024, 4:46am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/22 "2024-12-20T04:46:11Z")
Now I’m using 2024.4,you mean the 2025-beta? ---
**Author:** ![ZiruiDong](https://avatars.discourse-cdn.com/v4/letter/z/aeb1de/32.png) [@ZiruiDong](https://gromacs.bioexcel.eu/u/ZiruiDong)\ **Post date:** [December 20, 2024, 6:38am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/23 "2024-12-20T06:38:49Z")
sorry my fault ---
**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:** [December 21, 2024, 2:53am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/24 "2024-12-21T02:53:08Z")
Your screenshot says you are using 2021.3-bioconda. I’m suggesting you compile version 2024.4 from source, not a beta version. If you can reproduce the problem with 2024.4, that’s useful to know. I can’t see a reason why this would be happening. ---
**Author:** ![sizhe\_Li](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sizhe\_Li](https://gromacs.bioexcel.eu/u/sizhe_Li)\ **Post date:** [December 24, 2024, 3:37am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/25 "2024-12-24T03:37:13Z")
Also some questions want to ask: The Error show me some errors like this, and this PDB are from AlphaFold Database.Can i add HB3 item in aminoacids.rtp of force field？ ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/5ba5412411cc020e8eec38a72c3db25a2b9f4318.png) ---
**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:** [December 25, 2024, 3:18am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/26 "2024-12-25T03:18:27Z")
I do not advise changing the force field residue definitions. This is a textbook case for `-ignh`. ---
**Author:** ![sizhe\_Li](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sizhe\_Li](https://gromacs.bioexcel.eu/u/sizhe_Li)\ **Post date:** [December 25, 2024, 8:33am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/27 "2024-12-25T08:33:10Z")
Although it look like some hydrogen atoms? Most cases are HB3, HG3, HD3? ---
**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:** [December 26, 2024, 2:39am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/28 "2024-12-26T02:39:19Z")
Yes, it is a hydrogen atom. Some programs and nomenclature systems use e.g. HB2 and HB3 for H atoms attached to the Cβ atom, but GROMACS and all its constituent force fields use HB1 and HB2, instead. ---
**Author:** ![sizhe\_Li](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sizhe\_Li](https://gromacs.bioexcel.eu/u/sizhe_Li)\ **Post date:** [December 26, 2024, 2:47am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/29 "2024-12-26T02:47:11Z")
So can I refer to the existing parameters of HB and HB2 content in the force field file to add HB3? ---
**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:** [December 27, 2024, 2:14am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985/30 "2024-12-27T02:14:04Z")
Again, I do not advise editing the force field files. You don’t need to, and this is a manual and error-prone task. Please use `-ignh` (and solve the underlying issue first, if that is still needed - I’m not clear as to whether that has been resolved yet). The option is designed **exactly** for this situation. [Previous page](https://gromacs.bioexcel.eu/t/protein-protein-interaction-tutorial/8985.md?page=1)