# Efficient Workflow for Multiple Modified Residues
**URL:** https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565
**Category:** User discussions
**Created:** [June 29, 2026, 7:20am UTC](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565 "2026-06-29T07:20:39Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@marusya](https://gromacs.bioexcel.eu/u/marusya)
#### Post date: [June 29, 2026, 7:20am UTC](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565/1 "2026-06-29T07:20:39Z")
GROMACS version: 2022.4
GROMACS modification: No
Hi all,
I need to perform molecular dynamics simulations of multiple ligands that are covalently attached to cysteine residues. Is there an automated way to generate the parameters for these modified residues and integrate them into a force field, rather than manually creating and adding the parameters for each modified residue?
Any recommendations or suggested workflows would be greatly appreciated.
Thanks!
Marusya
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### Author:  [@Karis](https://gromacs.bioexcel.eu/u/Karis)
#### Post date: [June 29, 2026, 7:53am UTC](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565/2 "2026-06-29T07:53:59Z")
There are automated tools available online for each forcefield, see [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/02_topology.html) , if you have the coordinate file for the molecule, these should work to generate the parameters you need.
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### Author:  [@JonahC](https://gromacs.bioexcel.eu/u/JonahC)
#### Post date: [July 1, 2026, 10:17am UTC](https://gromacs.bioexcel.eu/t/efficient-workflow-for-multiple-modified-residues/13565/3 "2026-07-01T10:17:01Z")
gromologist is the tool you want here