# Proein-protein interaction procedure
**URL:** https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864
**Category:** User discussions
**Created:** [December 20, 2024, 6:43am UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864 "2024-12-20T06:43:25Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@ZiruiDong](https://gromacs.bioexcel.eu/u/ZiruiDong)
#### Post date: [December 20, 2024, 6:43am UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864/1 "2024-12-20T06:43:25Z")
GROMACS version:2024.4z
GROMACS modification: No
Hello all, when I conduct protein-protein interaction after finishing gromac tutorial of protein-ligand interaction, I stuck at here. In the tutorial, it writes:The ligand introduces new dihedral parameters, which were written to “jz4.prm” by the cgenff\_charmm2gmx.py script. At the TOP of topol.top, insert an #include statement to add these parameters:
; Include forcefield parameters
#include “./charmm36-jul2022.ff/forcefield.itp”
; Include ligand parameters
#include “jz4.prm”
[moleculetype]
; Name nrexcl
Protein\_chain\_A 3
However, when the other ligand is another protein (not small molecules), how could I add this parameter(since there is no proteinB.prm after I conduct both protein using the following command: “gmx pdb2gmx -f proteinA\_clean.pdb -o proteinA\_processed.gro -p protein.top -ter” and" gmx pdb2gmx -f proteinB\_clean.pdb -o proteinB\_processed.gro -p proteinB.top -ter"
Whatsmore,Another problem I encountered is that it seems wrong to add
; Include Position restraint file
#ifdef POSRES
#include “proteinA.itp”
#endif
; Include ligand topology
#include “proteinB.itp”
; Include water topology
#include “./charmm36-jul2022.ff/tip3p.itp”
under this circumstances as tutorial, what change should I conduct accordingly?
Above all, when conducting protein-protein interaction, whats the difference step from gromacs tutorial’s protein-ligand interaction when establishing complex topology file?
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 21, 2024, 2:53am UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864/2 "2024-12-21T02:53:45Z")
If you have multiple protein chains, just run the whole complex through `pdb2gmx`. The protein-ligand tutorial does not apply at all in that case.
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### Author:  [@ZiruiDong](https://gromacs.bioexcel.eu/u/ZiruiDong)
#### Post date: [December 21, 2024, 1:26pm UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864/3 "2024-12-21T13:26:01Z")
thanks for replying, but how could I have the complex when I only have two seperate protein file? For example. protein\_A.pdb and protein\_B.pdb.
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 22, 2024, 3:29am UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864/4 "2024-12-22T03:29:57Z")
You need to provide them as a single PDB file to `pdb2gmx`. The program can handle multiple chains in a single file as long as they have different chain ID or are separated by TER cards.
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### Author:  [@ZiruiDong](https://gromacs.bioexcel.eu/u/ZiruiDong)
#### Post date: [December 25, 2024, 12:57pm UTC](https://gromacs.bioexcel.eu/t/proein-protein-interaction-procedure/10864/5 "2024-12-25T12:57:41Z")
Thanks for your help!!!