Computational methods - FeS patching

CHARMM parameter and topology files for the FeS clusters were taken from:

Chang, C. H., & Kim, K. (2009). Density functional theory calculation of bonding and charge parameters for molecular dynamics studies on [FeFe] hydrogenases. Journal of Chemical Theory and Computation, 5(4), 1137–1145.
(Ref. 65)

FeS Cluster Integration and Patching Protocol

The first step in system construction involved writing each protein chain and its associated cofactors to separate PDB files. We used the VMD plugin PSFGEN to construct the topology, with each chain defined as a separate segment. The basic syntax is:

segment CHAK {
 pdb CHAK.pdb
}
coordpdb CHAK.pdb CHAK

Cofactors were added in their own segments. Patches were applied using PRES entries from the topology file. For example, FeS cluster patching was done as follows:
 

segment CHA1 {
 pdb CHA1.pdb
}
coordpdb CHA1.pdb CHA1
 

segment COF1 {
 auto none
 pdb ../FeSCLUSTERS/CHA1_FeS_coord.pdb
 first none
 last none
}
patch F4-1R COF1:501 CHA1:427
patch F4-4R COF1:501 CHA1:387
patch F4-2R COF1:501 CHA1:381
patch F4-3R COF1:501 CHA1:384
coordpdb ../FeSCLUSTERS/CHA1_FeS_coord.pdb COF1

Notes:

• Do not use regenerate angles dihedrals after FeS patching, as this can overwrite the custom bonding and angles defined in the parameter files.
• After patching, you must rename the segment of the cofactor atoms to match the protein segment before writing the PSF. For example:

set prot1 [atomselect top "segname CHA1 COF1"]
$prot1 set segname CHA1
 

This ensures that FeS cluster atoms are treated as part of the main protein chain in downstream topology.

Conversion to GROMACS

The resulting PSF  files were converted to GROMACS format using the script psf2itp.py, available from the CHARMM-GUI website. This generated .itp files for all components, preserving patches and segment consistency.

From here, the system was minimized, equilibrated, and simulated using GROMACS v2020.3 as described in the main methods section.