The Electrostatic Tools were used in the project of modification of AutoDock to make it halogen-bonding-aware. The idea of the modification is in addition of multipole charge custers (MCCs) to the halogens to simulate their intristic quadrupole moment.
In this project the Electrostatic Tools were used as a python library for molecule preparation purposes for modified AutoDock docking program. The AutoDock was patched to allow correct treatment of the MCCs. The patch file can be downloaded here.
You can use the scoring function obtained in this work for your own purposes. To do so download the a sample archive with a helper scripts.
You will find two directories in this archive:- scripts is a directory, containing all the scripts needed for fast scoring of a library of from the pdbbind database with both normal AutoDock and AutoDock-XB scoring functions. Note, that you need a patched version of AutoDock for correct energies.
- lib is a directory containing two sample entries from the PDBbind database.
To try working with AutoDock-XB scoring function untar the archive and in the ad-xb_sample directory issue the following commands (assuming your shell is bash)
mkdir ad-xb cd ad-xb ../scripts/prepare.sh ../lib mcc $(ls ../lib)The scripts assume AutoDock tools scripts are available in you
PATH. If not you can set
the AD_ROOT enviromental variable with path to these scripts.
The "prepare.sh" script prepares the structure set for scoring calculation
(just like it is described in the original ad-xb article). In the case of the command entered
above it will use the AutoDock-XB scoring function, because the mcc keyword was provided,
it wil use the ../lib directory as the one, contaning PDBbind database, and it will
extract every complex from the ../lib directory, because a listing of this directory
($(ls ../lib)) was provided as a list of pdb codes for scoring.
The script will create a directory per each complex and fill it with *.pdbqt files and a
directories with *.gpf and *.dpf files for each of six grids
(as described in the original article.
To perform the scoring calculation, issue the command:
../script/calc.sh $(ls)This script will run a several parallel calculation processes which number should be equal to your CPU cores. The number of parallel processes can be overriden with
NPROC
environmental variable. The $(ls) specifies which complexes are to be calculated
(all the complexes in the current directory in our case).
Note that you will see the warning of nonintegral ligand charge. These warning are normal.
They are present due to the limitations of the pdbqt file format. The extra-points in
the MCC model get the extremely high charge (tens and hundreds of a.u.), but the width of the
atom charge field in the pdbqt format is limited, so a truncation of these values are
inevitable. This truncation leads to nonintegral charge. If you are worried, you can try to increase
the MCC radius by modifying the mmol2mol call in the prepare_ligand.py
script.
Al last, to extract the calculated data issue:
../scripts/analyze.sh mcc $(ls)This script will extract the scores from the AutoDock outputs, perform corection on torsional degrees of freedom in the case of AutoDock-XB scoring function and print the results as a table. The torsional correction is needed since 2 torsions are added per halogen atom with MCCs. These torsions are frozen in docking experiments, however they are included in the score by AutoDock and their contribution must be removed from the score, since they have no physical meaning.
With some coding experience present, these scripts can be easily modified to eliminate the six grids, or to perform docking simulations.