# Using the Martini3 Forcefield in pdb2gmx

**URL:** <https://gromacs.bioexcel.eu/t/using-the-martini3-forcefield-in-pdb2gmx/10862>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [December 19, 2024, 6:31pm UTC](https://gromacs.bioexcel.eu/t/using-the-martini3-forcefield-in-pdb2gmx/10862 "2024-12-19T18:31:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![zamydm](https://avatars.discourse-cdn.com/v4/letter/z/e47c2d/32.png) [@zamydm](https://gromacs.bioexcel.eu/u/zamydm)\
**Post date:** [December 19, 2024, 6:31pm UTC](https://gromacs.bioexcel.eu/t/using-the-martini3-forcefield-in-pdb2gmx/10862/1 "2024-12-19T18:31:52Z")

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GROMACS version: 2023.4  
GROMACS modification: No  
Good morrow everyone!

I have been trying to generate an itp file for a coarse grained protein I converted using Charmm-Gui, and to do so I have been attempting to use pdb2gmx with the martini3 force field. I did not use Martinize2 on account of some elements of my protein structure being incompatible.

For the life of me I cannot get pdb2gmx to recognize the martini3 force field in the directory. I am using the version found here: [Particle definitions – Martini Force Field Initiative](https://cgmartini.nl/docs/downloads/force-field-parameters/martini3/particle-definitions.html) . I have attempted using the whole package, just the force field file, and some combination of the two and it just won’t recognize the force field. I have also tried naming the folder both martini3001 or martini3001.ff and both fail. Any assistance in this issue would be appreciated.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [January 7, 2025, 8:51am UTC](https://gromacs.bioexcel.eu/t/using-the-martini3-forcefield-in-pdb2gmx/10862/2 "2025-01-07T08:51:57Z")

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As far as I know, you can’t use `pdb2gmx` to generate Martini topologies. I think you’ll have to use specific Martini tools, such as `martinize` and `insane`. Have you read [GROMACS Tutorial: Coarse-Grained Simulations with Martini 3 Force Field - Compchems](https://www.compchems.com/gromacs-tutorial-coarse-grained-simulations-with-martini-3-force-field/#coarse-grained-simulations)?

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**Author:** ![zamydm](https://avatars.discourse-cdn.com/v4/letter/z/e47c2d/32.png) [@zamydm](https://gromacs.bioexcel.eu/u/zamydm)\
**Post date:** [January 7, 2025, 7:55pm UTC](https://gromacs.bioexcel.eu/t/using-the-martini3-forcefield-in-pdb2gmx/10862/3 "2025-01-07T19:55:34Z")

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Thank you for the reply. I resolved my issue, I just had to use a different method to repair my protein. Thank you for the link as well. I have seen it, however the issue I was having was separate from that tutorial.