# Why we are using GROMACS protein-ligand tutorial? **URL:** \ **Category:** User discussions\ **Created:** [October 9, 2023, 12:05pm UTC](https://gromacs.bioexcel.eu/t/why-we-are-using-gromacs-protein-ligand-tutorial/7353 "2023-10-09T12:05:57Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![pelinsu](https://avatars.discourse-cdn.com/v4/letter/p/5fc32e/32.png) [@pelinsu](https://gromacs.bioexcel.eu/u/pelinsu)\ **Post date:** [October 9, 2023, 12:05pm UTC](https://gromacs.bioexcel.eu/t/why-we-are-using-gromacs-protein-ligand-tutorial/7353/1 "2023-10-09T12:05:58Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I followed the protein-ligand complex tutorial. It worked but I can’t calculate the rmsd of the ligand. The tutorial seems incomplete to me at this part. Is reindexing necessary? When I want to make a selection after re-indexing, I get the following error. ![WhatsApp Image 2023-10-09 at 12.02.42](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0d728922756d00bfe8acff3ee05d491b50c5574f.jpeg) Which options should I consider to buy lignd’s rmsd? ---
**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:** [October 9, 2023, 1:35pm UTC](https://gromacs.bioexcel.eu/t/why-we-are-using-gromacs-protein-ligand-tutorial/7353/2 "2023-10-09T13:35:12Z")
> [@pelinsu](#): > > The tutorial seems incomplete to me at this part. I would appreciate any feedback you have as to why you consider this part incomplete. > [@pelinsu](#): > > Is reindexing necessary? To compute the RMSD of only the non-hydrogen atoms, yes. This is standard practice as H positions are not experimentally assigned in this case so using them for RMSD is a bit suspect. Your command appears to have worked fine, but the warning (not error) means you likely did not save all of the atoms in your trajectory file when running MD or from some post-processing step with `trjconv`. This means the contents of the `.tpr` file (topology) do not match that of the trajectory, and the program is warning you about this in case it may cause a problem. For your case, it did not. ---
**Author:** ![pelinsu](https://avatars.discourse-cdn.com/v4/letter/p/5fc32e/32.png) [@pelinsu](https://gromacs.bioexcel.eu/u/pelinsu)\ **Post date:** [October 9, 2023, 1:53pm UTC](https://gromacs.bioexcel.eu/t/why-we-are-using-gromacs-protein-ligand-tutorial/7353/3 "2023-10-09T13:53:43Z")
> [@jalemkul](#): > > To compute the RMSD of only the non-hydrogen atoms, yes. This is standard practice as H positions are not experimentally assigned in this case so using them for RMSD is a bit suspect. > > Your command appears to have worked fine, but the warning (not error) means you likely did not save all of the atoms in your trajectory file when running MD or from some post-processing step with `trjconv`. This means the contents of the `.tpr` file (topology) do not match that of the trajectory, and the program is warning you about this in case it may cause a problem. For your case, it did not. Thanks a lot. So which commands should I use to calculate RMSD for ligand to protein ? while I am calculating rmsd value from .xtc and .tpr files, Have they include protein and ligand complex? ---
**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:** [October 9, 2023, 5:26pm UTC](https://gromacs.bioexcel.eu/t/why-we-are-using-gromacs-protein-ligand-tutorial/7353/4 "2023-10-09T17:26:40Z")
> [@pelinsu](#): > > So which commands should I use to calculate RMSD for ligand to protein ? If you want to compute the ligand RMSD after fitting to the protein, that’s precisely what the tutorial has you do. Doing so gives you the ability to see how much the ligand deviated from its original pose after removing overall motion of the protein. Is this not what you want?