# Complex protein ligand Issue **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, analysis-tools, simulation-setup\ **Created:** [September 26, 2024, 11:20am UTC](https://gromacs.bioexcel.eu/t/complex-protein-ligand-issue/10239 "2024-09-26T11:20:04Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Sakho](https://avatars.discourse-cdn.com/v4/letter/s/9de0a6/32.png) [@Sakho](https://gromacs.bioexcel.eu/u/Sakho)\ **Post date:** [September 26, 2024, 11:20am UTC](https://gromacs.bioexcel.eu/t/complex-protein-ligand-issue/10239/1 "2024-09-26T11:20:04Z")
Hello everyone, I would like to ask if the following behavior is normal when building a ligand-protein complex in GROMACS. I am following the standard procedure: 1. I run the command `gmx pdb2gmx -f PRO.pdb -o PRO_processed.gro` for the protein ( charmm36 ff). 2. Then, for the ligand, I use `gmx editconf -f LIG.pdb -o LIG.gro`. After that, I form the ligand-protein complex by adding the specific content of LIG.gro into PRO\_processed.gro. However, when I visualize the result (complex.gro), I get an unexpected image. In other tests I’ve performed with the same protein and two different ligands, one ligand sits directly in the protein while the other is positioned at a relatively long distance. Here are the file contents and the image: [Attach File and image](https://drive.google.com/drive/folders/18W7Va3n8ZQBdrhEdqahq8WS1MrZkfqih?usp=drive_link) Thanks ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 1, 2024, 8:56am UTC](https://gromacs.bioexcel.eu/t/complex-protein-ligand-issue/10239/2 "2024-10-01T08:56:48Z")
To avoid other people answering in this thread, I think this issue was resolved (as one of the issues) in [Error Coordinat not matching gromacs](https://gromacs.bioexcel.eu/t/error-coordinat-not-matching-gromacs/10231).