Question: What is a .pqr file?
Answer:
A .pqr file is an ascii text file containing position-coordinates (p),
partial atomic charges (q), and atom size (r) for atoms in the molecule.
Question: Does BION-2 accept .pqr files with missing hydrogen?
Answer: NO. Hydrogen atoms must be present.
Question: What about missing residues?
Answer:
Missing residues must be modeled before generating .pqr.
Question: Can atom sizes be zero?
Answer: NO. Zero atom size is unphysical.
Question: Small molecules bound to protein?
Answer:
Supported, as long as p, q, r values exist in the .pqr file.
Question: Can all charges be zero?
Answer: NO. Charge information is required.
Question: Why .pqr instead of .pdb?
Answer:
.pqr allows incorporating protonation state and pH effects.
Question: How to generate .pqr?
Answer:
Use tools like
DelphiPka,
pdb2pqr, or Reduce.
