PDB2PQR takes PDB files as input, and output PQR files. PQR files differ from PDB in that they contain the charge state of each atom. PQR files are used to compute the electric fields around a protein using APBS and VMD.

• Download and prepare the PDB structure file for your molecule
  • Download PDB files here: protein databank
  • This step is the hardest and most crucial part of the process. You must ensure that the protein structure is what you think it is. Some common things to looks out for:
    • Is the structure from a different animal from what you're after?
    • Is the structure a mutant of the one you're after? (look for letter-number-letter codes which summarize mutations. i.e. G134A means that residue 134 is mutated from glycine to alanine).
    • Is the structure the complete structure, or is it a fragment or missing some residues?
      • It's very common that some residues don't crystallize, meaning the residues 'freeze' into different configurations in each unit cell. In that case, x-ray diffraction experiments can't get information on those residues. This is especially common near the ends of the peptide chain (the first and last ~10 residues), but can also happen in loops in the middle of the protein. You can get this sort of information from the Molecular Description tab on the structures page on the protein data bank.

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• Are there any other molecules in the PDB file besides your protein?
  • Oftentimes, other molecules crystalize with the protein and are contained in the PDB file. Sometimes this is intentional (i.e to study the interaction between two molecules), And sometimes it is not (i.e. waters, ions, etc.). Also, be aware that multiple copies of the protein may exist in the file (this happens when more than one protein crystalize in the unit cell). These extraneous molecules will need to be removed from the PDB file in advance. This is most easily done by loading the PDB file up in VMD and then saving a subset of ions to a new PDB file.
    • With a PDB file loaded up in VMD, highlight your molecule in the VMD Main window and select File → Save Coordinates…. In the Save Trajectory dialog box specify the atoms you want saved. You can use all of the atom selection commands which are used in the Graphical Representations dialog box (i.e. chain A, resid>100 and resid<150, etc.)
• With the PDB preparation done, it's time to convert to a PQR file. The conversion can be done online here: Online PDB2PQR. Or locally from here: Local PDB2PQR.
• Type in PDB # or upload PDB file
• Choose PARSE for force field
• Choose the internal naming scheme
• Use PROPKA to assign a pH value for the environment
• The output filetype is .pqr
• Look at .pqr file header to check for any errors
• PDB2PQR is very picky about what residue codes are used in the PDB files. If an error occurred the offending residues may need to be renamed in the PDB file or a .mol2 file needs to be supplied to PDB2PQR so it knows how to deal with them. Some residues can be built and have .mol2 files generated by PRODRG.
• The output PQR file contains the total charge of the molecule in the header. Below that, the partial charge of each atom is listed along with it's coordinates (second column from the left).