Using the Martini3 Forcefield in pdb2gmx

User discussions
1

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 . 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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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?

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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.