How to keep chain ID / IDs in GROMACS?

In GROMACS, while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL.

There are two ways to convert .gro file into .pdb

Lets say your protein name is xyz.pdb

1] gmx editconf -f xyz.gro -o xyz.pdb

2] gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr

Only 'trjconv' will retrieve the chain ID information for all the chains. and not 'editconf'.

If you have monomer protein and wish to assign any chain ID then following command will be of your interest:

gmx editconf -f xyz.gro -o xyz.pdb -label [chain-ID]

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