pdbfixer 1.12.0

Protein Data Bank (PDB) files often have a number of problems that must be fixed before they can be used in a molecular dynamics simulation. The details vary depending on how the file was generated. Here are some of the most common ones:

• If the structure was generated by X-ray crystallography, most or all of the

• hydrogen atoms will usually be missing.

• There may also be missing heavy atoms in flexible regions that could not be clearly resolved from the electron density. This may include anything from a few atoms at the end of a sidechain to entire loops.

• Many PDB files are also missing terminal atoms that should be present at the ends of chains.

• The file may include nonstandard residues that were added for crystallography purposes, but are not present in the naturally occurring molecule you want to simulate.

• The file may include more than what you want to simulate. For example, there may be salts, ligands, or other molecules that were added for experimental purposes. Or the crystallographic unit cell may contain multiple copies of a protein, but you only want to simulate a single copy.

• There may be multiple locations listed for some atoms.

• If you want to simulate the structure in explicit solvent, you will need to add a water box surrounding it.

PDBFixer can fix all of these problems for you in a fully automated way. You simply select a file, tell it which problems to fix, and it does everything else.