I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring function to take a look at the energy components - I don't want to re-dock the ligands into the protein binding sites.

From what I have found on the internet, I came up with this procedure, but I am not sure if this is the right approach, and also I get an error in the last step saying that "atoms are outside the grid".

autodock rescoring steps

1. Preparing the receptor

• need to add hydrogens if not present
• adds gasteiger charges to peptide

input:

• protein.pdb

output:

• protein.pdbqt

script:

prepare_receptor4.py -r protein.pdb [options]

2. Preparing the ligand

• add hydrogens if not present

input:

• ligand.pdb or ligand.mol2

output:

• ligand.pdbqt

script:

prepare_ligand4.py -l ligand.mol2 [options]

3. Generate grid parameter file

inputs:

• ligand.pdbqt
• protein.pdbqt

output:

• protein.gpf

script:

prepare_gpf4.py -l ligand.pdbqt -r protein.pdbqt [options]

4. AutoGrid: generate maps and grid data file

inputs:

• protein.pdbqt
• protein.gpf

outputs:

• protein.glg Grid Log File
• protein.*.map affinity maps for different atoms
• protein.maps.fld Grid data file
• protein.d.map desolvation map
• protein.e.map electrostatic map

command:

autogrid -p protein gpf

5. Generate docking parameter file

inputs:

• ligand.pdbqt
• protein.pdbqt

output:

• ligand_protein.dpf

script:

prepare_dpf4.py -l ligand.pdbqt -r protein.pdbqt [options]

6. Prepare .dpf file and run autodock for re-scoring

Remove seach parameters and append the "epdb" keyword, so that an examplary .dpf would look like this:

autodock_parameter_version 4.2 # used by autodock to validate parameter set
outlev 1                             # diagnostic output level
intelec                              # calculate internal electrostatics
ligand_types C HD N NA OA            # atoms types in ligand
fld rec.maps.fld                 # grid_data_file
map rec.C.map                    # atom-specific affinity map
map rec.HD.map                   # atom-specific affinity map
map rec.N.map                    # atom-specific affinity map
map rec.NA.map                   # atom-specific affinity map
map rec.OA.map                   # atom-specific affinity map
elecmap rec.e.map                # electrostatics map
desolvmap rec.d.map              # desolvation map
move lig.pdbqt                       # small molecule
about 17.6 22.2 32.6         # small molecule center
epdb                                   # small molecule to be evaluated

inputs:

• ligand_receptor.dpf

command:

autodock -p ligand_protein.dpf