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

Paul bauer paul.bauer.q at gmail.com
Mon Aug 24 08:40:06 CEST 2020


it is better to ask this stuff at the forum (gromacs.bioexcel.eu) now 
and maybe repeat the question there, or check if there are similar 
questions already.

This list is only for things related to the GROMACS software development :)

If you think that the behavior you describe is a bug, please check the 
open issues here (https://gitlab.com/gromacs/gromacs/-/issues) if 
something similar has already been filed and if not open a new issue for it.



On 23/08/2020 12:53, Sridhar Acharya Malkaram wrote:
> 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
> 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

Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab

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