# How to build 2Fe-2S cluster model for simulation?
**URL:** https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971
**Category:** User discussions
**Tags:** forcefield, simulation-setup
**Created:** [March 14, 2023, 7:29am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971 "2023-03-14T07:29:10Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@Wentao](https://gromacs.bioexcel.eu/u/Wentao)
#### Post date: [March 14, 2023, 7:29am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/1 "2023-03-14T07:29:10Z")
GROMACS version: 2022.5
Related software: ACPYPE, Ambertools22, Gaussian16
The protein I am interested in is PDB:6B6G. There is a 2Fe-2S cluster locating at the center of the protein and the two ion atoms interact with two deprotonated CYS repectively.
I already get some parameters from literature and DFT calculation related to the 2Fe2S - 4CYS. Now I would like to embed these bond parameter into ff99sb-ildn force field. How should I build this model for the gromacs simulation? Which of the topology files should be modified?
Thanks for helping!
---
### Author:  [@Wentao](https://gromacs.bioexcel.eu/u/Wentao)
#### Post date: [March 16, 2023, 7:04am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/2 "2023-03-16T07:04:03Z")
I write several .itp files. First is the **topol.top** :
; Include forcefield parameters
#include “amber99sb.ff/forcefield.itp”
; Include custom atom type
#include “dummy.itp”
#include “atomtype\_FES.atp”
; Include chain topologies
#include “topol\_chain\_C\_modified.itp”
#include “topol\_chain\_D\_modified.itp”
; Include FES cluster topology
#include “FeS.itp”
#ifdef POSRES\_FES
#include “posre\_FeS.itp”
#endif
#include “CYS-Fes.itp”
For **dummy.itp** , I just replace the H atom of Cys residue by dummy atom. It is shown here:
[atomtypes]
; name at.num mass charge ptype sigma epsilon
DUM 0 0.001 0.000 A 0.00000 0.00000
For **atomtype\_FES.itp** :
; atomtype\_FES.atp
; Custom atom types for Fe and SF atoms
[atomtypes]
; name at.num mass charge ptype sigma (nm) epsilon (kJ/mol)
Fe 26 55.84500 0.6004 A 1.40000 0.01571
SF 16 32.06500 -0.5164 A 2.00000 0.25000
---
### Author:  [@Wentao](https://gromacs.bioexcel.eu/u/Wentao)
#### Post date: [March 16, 2023, 7:06am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/3 "2023-03-16T07:06:23Z")
Topol of chain C and D are generated by pdb2gmx, but I replace the target Cys H bond with dummy atom.
The **FES.itp** :
[moleculetype]
; Name nrexcl
FES 3
[atoms]
; id type resnr residue atom cgnr charge mass
1 SF 1 FES S1 1 -0.51640 32.065
2 SF 1 FES S2 2 -0.51640 32.065
3 Fe 1 FES FE1 3 0.60040 55.845
4 Fe 1 FES FE2 4 0.60040 55.845
[bonds]
; i j func b0 (nm) kb (kJ/mol nm^2)
1 3 1 0.22 39080
2 4 1 0.22 39080
1 4 1 0.22 39080
2 3 1 0.22 39080
[angles]
; i j k func th0 (deg) cth (kJ/mol rad^2)
1 3 2 1 103 72.312
1 4 2 1 103 72.312
3 1 4 1 77 75.192
3 2 4 1 77 75.192
---
### Author:  [@Wentao](https://gromacs.bioexcel.eu/u/Wentao)
#### Post date: [March 16, 2023, 7:09am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/4 "2023-03-16T07:09:24Z")
Finally is the **CYS-Fes.itp** that I want to define the interaction between my cluster to the Cys residue:
[bonds]
; i j func b0 (nm) kb (kJ/mol nm^2)
FE1 SG3 1 0.22 34559
FE1 SG4 1 0.22 34559
FE2 SG1 1 0.22 34559
FE2 SG2 1 0.22 34559
[angles]
; i j k func th0 (deg) cth (kJ/mol rad^2)
SG3 FE1 SG4 1 108 273.967
SG1 FE2 SG2 1 108 273.967
S1 FE1 SG3 1 103 72.312
S1 FE1 SG4 1 103 72.312
S2 FE2 SG1 1 103 72.312
S2 FE2 SG2 1 103 72.312
[pairs]
; i j func
FE1 SG3 1
FE1 SG4 1
FE2 SG1 1
FE2 SG2 1
But it usually return warning that: Too few parameter …
---
### Author:  [@Wentao](https://gromacs.bioexcel.eu/u/Wentao)
#### Post date: [March 16, 2023, 7:11am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/5 "2023-03-16T07:11:42Z")
Now this system can be run by the software. But the result is not reasonable. The parameter are obtained frome papers.
---
### Author:  [@harsh\_v\_baid](https://gromacs.bioexcel.eu/u/harsh_v_baid)
#### Post date: [April 14, 2024, 2:33am UTC](https://gromacs.bioexcel.eu/t/how-to-build-2fe-2s-cluster-model-for-simulation/5971/6 "2024-04-14T02:33:53Z")
Hey ,
If you have somehow figured it then would you mind sharing the parameters and itp file