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convert_protein_to_pdbqt.readme.md

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docker image preparation

WORKDIR /opt RUN wget https://ccsb.scripps.edu/adfr/download/1038/ RUN mv index.html ADFR_install.tar.gz RUN tar -xzf ADFR_install.tar.gz WORKDIR /opt/ADFRsuite_x86_64Linux_1.0 RUN ./install.sh -d /opt/ADFRSuite

Convert PDB to PDBQT for AutoDock Vina-based docking (Conversion) This script takes a PDB file as input and optionally a boolean value describing whether hydrogens will be added to the structure. It then runs a file conversion step to create a PDBQT file that can be used to define the receptor for the docking.

  • Please carefully read through the conversation to see whether a pdb file is already downloaded. If not, please make sure to run "Download PDB File from RCSB Protein Data Bank using PDB Code" tool first to obtain a pdb file.
  • The input pdb file should be protein-only, which means the "Save a protein-only PDB file" should always be run beforehand to obtain a protein-only PDB structure
  • This is key to preparing a protein for docking

requirements

pdb-tools biopython