I am using autodock tools for molecular docking. After docking i am finding binding energy. I want the information regarding bond angle and bond length. is it possible with autodock?
Pranav Pandya, you can use Biovia discovery studio or Maestro from Schrodinger the free version of both of them they can provide you with the interaction diagram. or you can use Ligplot also a free tool used for interaction diagram with a citiation for it.citation
1- Discovery Studio visualizer, use receptor-ligand interactions > view interactions > define the receptor qnd ligand > define ligand > display receptor-ligand interactions > ligand interactions.
2- save the receptor and ligand in one file pdb, and open it with ligplot+, this software will give you the exact length.
3- save the receptor and ligand in one file pdb, and open it with pymol and use the command measure distance, and chose the two atoms which involved in bond formation.
Autodock refers to docking software, which docks the ligand with the macromolecule. To view the orientation and bond length visualizer also has to be used.