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

• Create a new directory containing the following input files to MakeDOCK:

1. rec.pdb: Prepared receptor file
2. xtal-lig.pdb: Ligand specification file

These are required to specify the target for docking. For help preparing these files, see #Receptor Preparation and #Ligand Preparation below.

How to use MakeDOCK

In the directory containing rec.pdb and xtal-lig.pdb.

setenv DOCK_BASE 

Receptor Preparation

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

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 hydrogens
5. Save as rec_original.pdb
6. Run 'paranoia.csh' to clean up the rec_original.pdb file into a rec.pdb file

Ligand Preparation

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

1. Delete everything BUT the ligand atoms
2. Save as xtal-lig.pdb