Hajar Chihab

Hello! I hope you doing well

First of all if you run auto dock tool so result file you can open by choosing lowest energy binding pose in DS, PyMol but on the other hand you have Autodock Vina so you open protein pdbqt file and ligand out file in PyMOL. And you wanna see the interaction between them so change the presentation through cartoon option. next you wanna merge both in one pdb so go through file option select export pdb option molecule as well as click on pdb option and check tick top3 option at end save in pdb file.

Use ChimeraX . Open the receptor file and drag the ligand pdbqt file directly to the window. Then select all and save as PDB.

OR

If you use Autodock 4, then you can save the complex using the dlg files.

OR

If you use Autodock Vina, then use vina_split and then use ChimeraX. (see above description).

PDB format is the text file. So, if both ligand and protein are in PDB format you can just append ligand file in the protein file and you can visualize the final file in chimera or any other visualization software.

Just open these files in any text editor like gedit/Wordpad/notepad/ etc. and copy-paste ligand file in the protein file in the last.

If you want to check receptor-ligand interaction you can do Protein-Ligand docking.Several online docking softwares such as Swiss-dock, Sanjeevini etc., are available.You can also try autodock( one of the best docking software- freeware)..you can define the binding site through literature search or ligand binding site prediction software...

Thank you all for your responses

both the files are text files and contain the coordinates of the amino acids, atoms etc.. so you could open the text files (provided both are in .PDB format) and copy the ligand file data to the protein text file.

you could visualise the file in tools like PyMOL to check if the file is proper after merging.