bio-otto/pdb_to_pdbqt

download and prepare a pdb file for docking wth Vina-flavoured algorithms

pdb_to_pdbqt

download and prepare a pdb file for docking wth Vina-flavoured algorithms

run notebook

user must input the PDB code (5WIU in the test case), and the ligand resname (AQD in the test case). If performing the optional step of parameterizing the ligand with GAFF (via openmmforcefields), user must also input the ligand isomeric SMILES code.

outputs in ./data/ are:

• 5wiu.pdb.gz - not really an output, it's just the compressed pdb file from the PDB
• protein.pdb - protein atoms only, aligned to the ligand's principal moment of inertia
• ligand.pdb - ligand only, aligned to the ligand's principal moment of inertia
• proteinH.pdb - protein only, missing atoms added by PDBFixer, and hydrogen's minimized by OpenMM. This is what you would use for docking.
• ligandH.pdb - ligand only, bond topology fixed by RDKit
• combined.pdb - protein, ligand, both with hydrogens, before minimizing.
• gaff_minimized.pdb - protein, ligand, both with hydrogens and minimized in vacuum without any constraints using GAFF-parameterized ligand

After this, one can generate the docking input file by:

obabel proteinH.pdb -xr -O proteinH.pdbqt

or use ODDT MolToPDBQTBlock