Loosing chain name in ".pdb" output after mdrun

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

I am using “.pdb” as the input and output structure format for my simulation, as I needed some useful features like chain-name.

Gromacs retains the chain information in output “.pdb” structures for many of its commands, but when I run mdrun, the output structure file “.pdb” (the option -c) has lost all chain information. I checked for any options that can be used to preserve chain information, but I found none.

I needed chain information in pdb format structure file, to properly generate index groups.

Is there a way to preserve chain information?

2

Have you gotten any solution?? would appreciate any help

3

I’m not sure there is a way to preserve chain information in mdrun, but it shouldn’t be necessary for any postprocessing. You can always create new index groups for each one of the chains separately using gmx make_ndx and selecting the appropriate residues/molecules for each chain.