# Performing MD for a protein-ligand complex where the protein is tetramer

**URL:** <https://gromacs.bioexcel.eu/t/performing-md-for-a-protein-ligand-complex-where-the-protein-is-tetramer/11046>\
**Category:** User discussions\
**Created:** [January 16, 2025, 3:28am UTC](https://gromacs.bioexcel.eu/t/performing-md-for-a-protein-ligand-complex-where-the-protein-is-tetramer/11046 "2025-01-16T03:28:13Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Abdulrahman](https://avatars.discourse-cdn.com/v4/letter/a/f19dbf/32.png) [@Abdulrahman](https://gromacs.bioexcel.eu/u/Abdulrahman)\
**Post date:** [January 16, 2025, 3:28am UTC](https://gromacs.bioexcel.eu/t/performing-md-for-a-protein-ligand-complex-where-the-protein-is-tetramer/11046/1 "2025-01-16T03:28:13Z")

</div>

GROMACS version: GROMACS - gmx pdb2gmx, 2023.3-Ubuntu\_2023.3\_1ubuntu3  
GROMACS modification: Yes/No

I am new to MD and GROMACS. I am performing molecular dynamics (MD) simulations for a protein-ligand complex, where the protein is a tetramer (chains A, B, C, and D). The ligand is docked to chain A.

During the step of adding the ligand parameters and topolgy to the system topology, I opened the topol.top file and found it to be different from the tutorial example. As a result, I was unsure where to paste the following two:

**; Include ligand topology #include “jz4.itp”**  
**; Include ligand parameters #include “jz4.prm”**

Here is the toplo.top file:

;  
; File ‘topol.top’ was generated  
; By user: unknown (0)  
; On host: LAPTOP-3GKP069M  
; At date: Tue Jan 7 23:52:28 2025  
;  
; This is a standalone topology file  
;  
; Created by:  
; :-) GROMACS - gmx pdb2gmx, 2023.3-Ubuntu\_2023.3\_1ubuntu3 (-:  
;   
; Executable: /usr/bin/gmx  
; Data prefix: /usr  
; Working dir: /mnt/c/Users/alaas/Desktop/EMPA\_MD  
; Command line:  
; gmx pdb2gmx -f REC.pdb -o REC\_processed.gro -ter  
; Force field was read from the standard GROMACS share directory.  
;

; Include forcefield parameters  
#include “charmm27.ff/forcefield.itp”

; Include chain topologies  
#include “topol\_Protein\_chain\_A.itp”  
#include “topol\_Protein\_chain\_B.itp”  
#include “topol\_Protein\_chain\_C.itp”  
#include “topol\_Protein\_chain\_D.itp”

; Ligand position restraints  
#ifdef POSRES

; Include water topology  
#include “charmm27.ff/tip3p.itp”

#ifdef POSRES\_WATER  
; Position restraint for each water oxygen  
[position\_restraints]  
; i funct fcx fcy fcz  
1 1 1000 1000 1000  
#endif

; Include topology for ions  
#include “charmm27.ff/ions.itp”

[system]  
; Name  
Protein in water

[molecules]  
; Compound #mols  
Protein\_chain\_A 1  
Protein\_chain\_B 1  
Protein\_chain\_C 1  
Protein\_chain\_D 1