# Protein that contains 4 chains with -ligand complex simualtion

**URL:** <https://gromacs.bioexcel.eu/t/protein-that-contains-4-chains-with-ligand-complex-simualtion/7664>\
**Category:** User discussions\
**Created:** [November 17, 2023, 9:33pm UTC](https://gromacs.bioexcel.eu/t/protein-that-contains-4-chains-with-ligand-complex-simualtion/7664 "2023-11-17T21:33:42Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![selo](https://avatars.discourse-cdn.com/v4/letter/s/5e9695/32.png) [@selo](https://gromacs.bioexcel.eu/u/selo)\
**Post date:** [November 17, 2023, 9:33pm UTC](https://gromacs.bioexcel.eu/t/protein-that-contains-4-chains-with-ligand-complex-simualtion/7664/1 "2023-11-17T21:33:42Z")

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GROMACS version: 2020  
GROMACS modification: Yes/No  
Here post your question  
Hello Everyone

I am doing protein-ligand simulation.  
My protein contains 4 chains A, B, C and D.  
i used **gmx pdb2gmx -f protein.pdb -o protein.gro -p topol\_protein.top -i posre\_protein.itp -ff amber99sb-ildn -water tip3p -ignh** to generate:  
topol\_Protein\_chain\_A.itp,  
posre\_Protein\_chain\_A.itp,  
topol\_Protein\_chain\_B.itp,  
posre\_Protein\_chain\_B.itp,  
topol\_Protein\_chain\_C.itp,  
posre\_Protein\_chain\_C.itp,  
topol\_Protein\_chain\_D.itp,  
posre\_Protein\_chain\_D.itp,  
protein.gro  
topol.top

My topol\_Protein\_chain\_A.itp looks like

 ![chain A](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/d/dd4d7a9a22315e0a52ddddf1ec00a7cb4b362933.png)

posre\_Protein\_chain\_A.itp,

 ![posre](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/3aa810acb5bea17e0a49e3e9e46cd25f013dcd45.png)

topol.top

 ![top2](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/ee3237ea8dafc50fe59b53f197e1ffbb2edb0797.png)  
 ![top1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/20e6ca15477f28545d524471b2fee27c39c68330.png)

I would like to know:

1. how i can merge my 4 .itp files ?
2. If my topology file is right

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 30, 2023, 8:08am UTC](https://gromacs.bioexcel.eu/t/protein-that-contains-4-chains-with-ligand-complex-simualtion/7664/2 "2023-11-30T08:08:17Z")

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Hi,  
GROMACS topology are hierarchical, that means the information ([directive]) in topol.top has to follow a predefined order. First forcefield descriptions, molecules description, system description  
To avoid to make to the file too long we use include to include the content from other files.  
Here you find details of topol.top format [https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html](https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html)

For example

- first the forcefield  
**#include “amber99sb-ildn.ff/forcefield.itp” :** this includes the information for the force field you are using, including bonded and non-bonded parameters
- molecule description for each molecule [moleculetype] [atoms] [bonds]…  
**#include topol\_Protein\_chain\_A.itp**  
**#include topol\_Protein\_chain\_B.itp**  
…
- last system description [molecules] that list all the molecules in the order they appear in the structure file.

Please check that your topol.top follows these rules, all the files are included and the order of the directive is correct in the file, if you have manually modified. From your post I could not understand the order of directive in your topol.top  
I hope it helps  
Alessandra