pdb file format
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
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.
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
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.