Port LignAmb25 Force Field to GROMACS

User discussions
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GROMACS version: 2026.0=nompi_cuda_h39c90b0_0
GROMACS modification: No

Dear community,

I would like to use the LignAmb25 force field in pdb2gmx.

Unfortunately, unlike CHARMM36, you can’t simply download the LignAmb25 force field and use it directly with the -ff option.

Although this page describes how to access AMBER force fields, it doesn’t include any forcefield.itp files, and the directory structure is completely different.

So far, I haven’t found a way to export the LignAmb25 force field so that it can be used with pdb2gmx -ff.

Hence my question: when will the LignAmb25 force field be officially included in GROMACS?

Robin

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@vedran Have you looked at LignAmb25?

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We have, but it is not high on our priority list. I might give it a go after we are done with DNA/RNA, but I am not deeply familiar with this class of molecules.

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While not a native solution, have you taken a look at Parmed ( GitHub - ParmEd/ParmEd: Parameter/topology editor and molecular simulator · GitHub ) for a short term solution?

Alternatively, given the complexity of lignin subunit linkages, if you wanted to be a bit more programmatic one of the polymer topology generators for gromacs might be better like PolyPly ( GitHub - marrink-lab/polyply_1.0: Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates · GitHub ) but you’ll need to generate the input definition files for the linkages and subunits by hand first.

Lignin, honestly, hasn’t had a whole lot of support in any MD engine and frequently, when I’ve had to run simulations containing lignin, I’ll either need to write a topology from scratch, or use something like ParmEd or topotools (built into VMD) to generate the correct topology files to match my structures from something like ligninbuilder.

As an aside, about 12 years ago, I had some residue definition files for the original CHARMM lignin force-field (not the most recent one from Vermaas) for use in GROMACS, but owing to the variety of inter-unit linkages, building (and updating) these files was non-trivial, though it might not be too difficult to generate the necessary definition files for pdb2gmx if the lignin you are trying to look at isn’t too messy (i.e. no branching, limited variety of linkages), it might be feasible to hack together a limited port.