Understanding MakeDOCK, which automates sphere and grid generation

What is MakeDOCK?

• MakeDOCK automates the process of sphere and grid generation for a target.

Input files to MakeDOCK

• The following files are required to specify the target for MakeDOCK:

1. rec.pdb: Prepared receptor file
2. xtal-lig.mol2 (or .pdb): Ligand specification file

Receptor Preparation

To prepare a typical pdb structure for use as the receptor in MakeDOCK, perform the following steps:

1. Remove solvent (i.e. crystallographic waters)
2. Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
3. Remove the ligand itself
4. Delete all hydrogen atoms
5. Save as rec_original.pdb

Ligand Preparations

To prepare the ligand specification, reload the original pdb structure and perform the following steps:

1. Delete everything BUT the ligand atoms
2. Add hydrogens and charges