pdb file format
Description
Files with the .pdb extension are molecular
structure files in the protein databank file format.  The protein
databank file format describes the positions of atoms in a molecular
structure. Coordinates are read from the ATOM and HETATM records,
until the file ends or an ENDMDL record is encountered.
GROMACS programs can read and write a simlation box in the
CRYST1 entry. 
The pdb format can also be used as a trajectory format:
several structures, seperated by ENDMDL, can be read from 
or written to one file.
Example
An pdb file should look like this
ATOM      1  H1  LYS     1      14.260   6.590  34.480  1.00  0.00
ATOM      2  H2  LYS     1      13.760   5.000  34.340  1.00  0.00
ATOM      3  N   LYS     1      14.090   5.850  33.800  1.00  0.00
ATOM      4  H3  LYS     1      14.920   5.560  33.270  1.00  0.00
...
...
speptide.pdb:
Protein structure file of Ribonuclease A speptide in protein data 
bank file format. 
Links to descriptions of the pdb format
can be found on the Links page.