pdb2gmx

From wiki.gromacs.org

This program reads a .pdb file, reads some database files, adds hydrogens to the molecules and generates coordinates in .gro format and a topology in .top format. These files can subsequently be processed by grompp to generate a run input file, tpr.

Note that a .pdb file is nothing more than a file format, and it need not necessarily contain a protein structure. Every kind of molecule for which there is support in the database can be converted, but if it is not there it will fail with an error. If there is no support in the database, you can add it yourself.

Typically used for large molecules that have repeating units or residues, such as proteins, DNA and polymers. Makes generation of the topology file easier / faster.

[edit] Reference

• Manual:pdb2gmx_3.3.2
• GROMACS Manual, Appendix D70
• pdb2gmx, Online ManualGenerating Topologies and Coordinates