# Simulating Protein-Ligand Interactions (Inhibition Mechanism) using GROMACS with a Mn cofactor/ion

**URL:** <https://gromacs.bioexcel.eu/t/simulating-protein-ligand-interactions-inhibition-mechanism-using-gromacs-with-a-mn-cofactor-ion/1016>\
**Category:** User discussions\
**Created:** [October 28, 2020, 6:36pm UTC](https://gromacs.bioexcel.eu/t/simulating-protein-ligand-interactions-inhibition-mechanism-using-gromacs-with-a-mn-cofactor-ion/1016 "2020-10-28T18:36:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bhaveshashok](https://avatars.discourse-cdn.com/v4/letter/b/b2d939/32.png) [@bhaveshashok](https://gromacs.bioexcel.eu/u/bhaveshashok)\
**Post date:** [October 28, 2020, 6:36pm UTC](https://gromacs.bioexcel.eu/t/simulating-protein-ligand-interactions-inhibition-mechanism-using-gromacs-with-a-mn-cofactor-ion/1016/1 "2020-10-28T18:36:24Z")

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GROMACS version: 2018.1  
GROMACS modification: No

Hello all,

I am trying to simulate the interactions between a ligand and the FTO Protein (PDB Code: 4ZS3) with a Manganese cofactor using the AMBER forcefield. I am unable to create a conf.pdb file using pdb2gmx because of the Mn ion. I know there is a way to manually add the parameters for this ion, but I do not know how. I have installed GROMACS onto my Linux Server (Ubuntu Bionic Beaver 18.04.4), and did not compile GROMACS - rather, I typed in gmx to the command line and was then prompted to install it using sudo apt install.

Any help regarding how to run this simulation would be appreciated.

Thank you in advance.

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**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 5, 2020, 9:38am UTC](https://gromacs.bioexcel.eu/t/simulating-protein-ligand-interactions-inhibition-mechanism-using-gromacs-with-a-mn-cofactor-ion/1016/2 "2020-11-05T09:38:53Z")

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Hi,  
In general, one has to be carefully in adding parameters to a force field. A requirement is that the ion parameters (e.i Mn) are compatible with the force field (e.i AMBER).  
Concerning how to add parameter to the gromacs force field file, here you can find some help

> **[Force field organization — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/reference-manual/topologies/force-field-organization.html)**

  
or  

> **[pdb2gmx input files — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html#pdb2gmxfiles)**

Best regards  
Alessandra