The term PDB can refer to the Protein Data Bank (http://www.rcsb.org/pdb/), to a data file provided there, or to any file following the PDB format. Files in the PDB include information such as the name of the compound, the species and tissue from which is was obtained, authorship, revision history, journal citation, references, amino acid sequence, stoichiometry, secondary structure locations, crystal lattice and symmetry group, and finally the ATOM and HETATM records containing the coordinates of the protein and any waters, ions, or other heterogeneous atoms in the crystal. Some PDB files include multiple sets of coordinates for some or all atoms. Due to the limits of x-ray crystallography and NMR structure analysis, the coordinates of hydrogen atoms are not included in the PDB.
NAMD and VMD ignore everything in a PDB file except for the ATOM and HETATM records, and when writing PDB files the ATOM record type is used for all atoms in the system, including solvent and ions. Here are the ATOM records for the first two residues of ubiquitin from the 1UBQ entry in the PDB:
ATOM 1 N MET 1 27.340 24.430 2.614 1.00 9.67 1UBQ 71 ATOM 2 CA MET 1 26.266 25.413 2.842 1.00 10.38 1UBQ 72 ATOM 3 C MET 1 26.913 26.639 3.531 1.00 9.62 1UBQ 73 ATOM 4 O MET 1 27.886 26.463 4.263 1.00 9.62 1UBQ 74 ATOM 5 CB MET 1 25.112 24.880 3.649 1.00 13.77 1UBQ 75 ATOM 6 CG MET 1 25.353 24.860 5.134 1.00 16.29 1UBQ 76 ATOM 7 SD MET 1 23.930 23.959 5.904 1.00 17.17 1UBQ 77 ATOM 8 CE MET 1 24.447 23.984 7.620 1.00 16.11 1UBQ 78 ATOM 9 N GLN 2 26.335 27.770 3.258 1.00 9.27 1UBQ 79 ATOM 10 CA GLN 2 26.850 29.021 3.898 1.00 9.07 1UBQ 80 ATOM 11 C GLN 2 26.100 29.253 5.202 1.00 8.72 1UBQ 81 ATOM 12 O GLN 2 24.865 29.024 5.330 1.00 8.22 1UBQ 82 ATOM 13 CB GLN 2 26.733 30.148 2.905 1.00 14.46 1UBQ 83 ATOM 14 CG GLN 2 26.882 31.546 3.409 1.00 17.01 1UBQ 84 ATOM 15 CD GLN 2 26.786 32.562 2.270 1.00 20.10 1UBQ 85 ATOM 16 OE1 GLN 2 27.783 33.160 1.870 1.00 21.89 1UBQ 86 ATOM 17 NE2 GLN 2 25.562 32.733 1.806 1.00 19.49 1UBQ 87
The fields seen here in order from left to right are the record type, atom ID, atom name, residue name, residue ID, x, y, and z coordinates, occupancy, temperature factor (called beta), segment name, and line number.
If this file is loaded into VMD and then written out as a new file, most of the extra information will be removed, the HETATM records will become ATOM records, and the previously empty chain ID field (between residue name and residue ID) will be set to X (unless present in the original file), and the line number will be omitted, as seen here:
ATOM 1 N MET X 1 27.340 24.430 2.614 1.00 9.67 1UBQ ATOM 2 CA MET X 1 26.266 25.413 2.842 1.00 10.38 1UBQ ATOM 3 C MET X 1 26.913 26.639 3.531 1.00 9.62 1UBQ