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PDB Files

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


next up previous
Next: PSF Files Up: NAMD Tutorial Previous: Acknowledgments
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