Efficient Workflow for Multiple Modified Residues

User discussions
1

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

2

There are automated tools available online for each forcefield, see Protein-Ligand Complex , if you have the coordinate file for the molecule, these should work to generate the parameters you need.