This is an updated to Python3 version of WaterDock2.0 https://github.com/bigginlab/WaterDock-2.0
If you still need the python2 version, you should visit: https://github.com/akshay-sridhar/WaterDock2.0
Original Python2 version of WaterDock2.0 written by Akshay Sridhar (https://doi.org/10.1371/journal.pone.0172743) based on the original WaterDock method developed by Greg Ross (https://doi.org/10.1371/journal.pone.0032036) Comments and queuries should be address to [email protected]
This is a Command line interface of WaterDock2.0 for python
python waterdock2.py proteinfile.pdbqt ligandfile.pdb
This will output a single file called "predictedwaters.pdb", which contains the predictions of the oxygen positions.
Example input files are included as example-protein.pdbqt and example-ligand.pdb
-- MDAnalysis (version >= 0.13)
-- numpy (any version compatible with your MDAnalysis build)
-- scipy (version does not matter)
-- vina (note on Mac Catalina, you may have to obtain the 64bit version directly from http://vina.scripps.edu/download.html)
Protein File -- pdbqt - the Autodock format of a PDB with charge (Q) and atom type (T)
Ligand File -- pdb/mol2 sybyl mol2 format
Note that both the ligand and the protein file should have the correction protonation state.
To generate the receptor pdbqt file, we recommend AutoDockTools (ADT - get MGLTools from http://mgltools.scripps.edu/downloads), but if you are on a Mac with Catalina there is currently no 64-bit version. In that case you might be avle to use the AFR package (see here https://ccsb.scripps.edu/adfr/how-to-create-a-pdbqt-for-my-receptor/)
An example protein (example-protein.pdbqt) and an example ligand are provide (example-ligand.pdb)
python waterdock2.py example-protein.pdbqt example-ligand.pdb
will generate predictedwaters.pdb which should contain 3 predicted water molecule locations.
You can check the result of the prediction in pymol or compare it directly to the file "expected-predictedwaters.pdb"