AutoDock is a software suite designed for simulating the molecular interactions between small ligands and protein targets. It can be used to predict the binding mode of a ligand to a protein target, as well as to estimate the binding affinity between the two molecules.
The input to AutoDock is a protein structure file and a ligand structure file, both of which should be in the PDB (Protein Data Bank) format. The output is a set of predicted docking poses, along with their corresponding binding energies.
Here is a basic script for running AutoDock:
```
autodock -p receptor.pdbqt -l ligand.pdbqt -o output.dlg
```
In this script, "receptor.pdbqt" is the protein structure file, "ligand.pdbqt" is the ligand structure file, and "output.dlg" is the output file where the predicted docking poses and their corresponding binding energies will be saved.
AutoDock also provides a number of options that can be specified in the command line to control the docking process. Some of the most commonly used options include:
- "-r seed": Set the random number generator seed for reproducibility
- "-n num_runs": Set the number of independent docking runs to perform
- "-N num_evals": Set the maximum number of energy evaluations for each docking run
- "-l num_confs": Set the maximum number of docking poses to output
- "-cpu num_cpus": Set the number of CPU cores to use for parallel docking
- "-v": Enable verbose output for debugging purposes
Here is an example script that includes some of these options:
```
autodock -p receptor.pdbqt -l ligand.pdbqt -o output.dlg -r 12345 -n 10 -N 2500000 -l 20 -cpu 4 -v
```
This script will perform 10 independent docking runs, each with a maximum of 2,500,000 energy evaluations. It will output up to 20 docking poses and use 4 CPU cores for parallel docking. Verbose output will be enabled for debugging purposes.
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