Dear Anupam Biswas , its normal to have the ligand far from the protein, it's just the preparative step, you have to prepare your ligand and protein set the gridbox, and start your docking, after that if your ligand is still far it means you have a problem. I advise you to do your Docking with Vina its more precise and easier to set up than the MGLTool, Use the latter just for the files prepâration and final visualization.

best regards

Anupam Biswas. It is a little bit technical. At first, find the active site of your protein. Set the grid box at the active site and follow the standard docking procedure. If the ligand comes to the position where it was previously present, your work is perfect. After that, you can go ahead. Best of luck.

Hey Anupam Biswas it's completely normal. When you import the ligands it will appear a bit apart from the protein structure. Once you have prepared the ligand and protein and set the grid box follow the standard docking procedure and you could see the ligand in the specified active site once you visualise the file after docking.

It is preprartive step when ligand far. In dlg file open in pymol see in movie you find in between