Does anyone know how to add the chain name into *.gro file?

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Justin Lemkul

The .gro file format does not (and cannot) make use of chain identifiers. If you want to use chain identifiers, use PDB format.

Vasiliy Triandafilidi

You can take advantage of such programs like MDAnalysis, which provide you with a powerful Python glue for MD analysis commands. In this link you can learn how to write a PDB file. Just before that use can use command

atoms=u.selectAtoms("all")

atoms.set_name("lalalal some string")

(there is also the same attribute for residues(chains) and etc)

http://code.google.com/p/mdanalysis/wiki/Examples