## pdb file format

Main Table of Contents | VERSION 4.0
GROMACS homepage | Sun 18 Jan 2009

### 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.

http://www.gromacs.org