GROMACS version: 2024.2
GROMACS modification: No
Hi everyone,
I’m currently working on a system that includes iron-sulfur clusters (2Fe2S, 4Fe4S, and 3Fe4S) coordinated by cysteine residues, and I’m using the CHARMM36-jul22 force field in GROMACS. Despite multiple attempts, I’m struggling to maintain the correct geometry of the clusters during energy minimization and MD simulations.
The main issue is that the Fe–S bonds within the clusters are defined and stable, but the Fe–SG bonds (between iron atoms and the sulfur of coordinating cysteines) are not preserved. I’ve tried defining these bonds in the [ intermolecular_interactions ] section at the end of the .top file, but it seems GROMACS doesn’t treat them as covalent bonds unless the atoms are part of the same molecule. I currently have separate .itp files for each cluster.
I would prefer to avoid merging the cluster and protein into a single molecule if possible, as the system also includes lipids. The entire system was prepared using CHARMM-GUI, and I manually inserted the clusters just before the initial minimization step.
Is there a way to define Fe–SG bonds directly in the .itp files or elsewhere so that GROMACS treats them as covalent? Alternatively, is there a recommended strategy for handling metal coordination in CHARMM36 within GROMACS?
Any advice, examples, or best practices would be greatly appreciated!
Thanks in advance,
Fulvio