pdb file format

Main Table of Contents VERSION 4.6
GROMACS homepage Sat 19 Jan 2013


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.


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.