[gmx-developers] Retaining chain name and original residue numbers in “.pdb” output after mdrun

Sridhar Acharya Malkaram smalkaram at wvstateu.edu
Sun Aug 23 12:53:21 CEST 2020

Hi gmx-developers,
I had originally posted this in the general mailing list, but without responses. I thought I might get a suggestion here. Any suggestion is appreciated.
GROMACS version: 2020.3
GROMACS modification: No
I am working on a scripted run of gromacs energy calculation (using gmx energy), to calculate energies for specific groups. I will be specifying in the energygrps option of the mdp to achieve this. However, I find a problem. The original residue numbers and chain names are no longer retained after the series of gromacscommands before  the gmx energy command.
I am using “.pdb” as the input and output structure format for my simulation to retain the 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?
Also, is there a way to prevent residue renumbering ? (Atom renumbering is not an issue)

With Kind Regards,

Sridhar A Malkaram, Ph.D.
Associate Professor,
Department of Mathematics and Computer Sciences
W729, Wallace Hall,
West Virginia State University,
Institute, WV-25112
Office: +1 (304)-766-5168
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