DOI: 10.25838/d5p-87
title: Data for "LignAmb25: A Comprehensive AMBER Force Field Addressing Lignin’s Structural and Chemical Diversity"

description: ############################################################################## SUPPORTING INFORMATION FOR THE LIGNAMB25 LIGNIN FORCE FIELD ############################################################################## #-- Please copy all .zip and .z0[1-5] files into one directory and start unpacking the .zip one with WinRAR. #--Molecules are named "PMxx" adhering to enumeration in Figure S5 ----------------------------- Archive structure ----------------------------- LignAmb25_SI # Contains data related to MEP reproduction of lignin multiomers ├── MEP-Comparison │   ├── Models # Mol2 files per lignin multimer + Gaussian output files per conformer │   ├── mep_reproduction_per_mol.csv # numerical data of the MEP reproduction of multimers ├── LignAmb25-Fragments.pdf # Visualization of LignAmb25 fragments with residue codes, atom types, atom names, and charges # Simulation data for the LignAmb25 validation (Crystal simualtions, delta Hvap, and delta HGyr estimation) # Contains pmemd input files + restart files per replica ├── MD-Simulations │   ├── Crystals │   ├── Delta-HGyr │   └── Delta-HVap # Amber-style dat, lib, and frcmod files for the AMBER-compatible and "standalone" versions of LignAmb25 ├── Parameter-Files │   ├── LignAmb25_HF │   └── LignAmb25_SOLO # PES Scan data for most model compounds used for optimization of bonded parameters └── PES-Scans ├── Angles ├── Bonds ├── Starting-Geometries ├── Torsion_fit_minmal.py # Script showcasing the torsion fitting procedure (not GPU-accelerated!) └── Torsions
description: LignAmb25 is a comprehensive force field for lignin molecular dynamics simulations implemented natively within the AMBER package. The force field includes parameters for all common monolignol units (p-coumaryl, coniferyl, caffeyl, and sinapyl alcohol) and their associated linkages (β O4, β 5, β β, β 1, 5 5, 5 O4, α-O4, BDO, and DBDO), along with less commonly encountered units such as tricin, spirodienones, and hydroxystilbenes. This enables simulations of both softwood and hardwood lignin structures with compositions that would be difficult to isolate experimentally. Force field parameters were initially derived from the GAFF2 force field and systematically optimized using quantum mechanical calculations at the ωB97X D4/def2 TZVPP level of theory on conformer ensembles derived via the CREST/CENSO conformational sampling toolchain. Partial atomic charges were derived using the RESP methodology, consistent with AMBER conventions. Experimentally measured crystal structures of lignin simulated with LignAmb25 accurately retain their packing based on calculations of the RMSD and density error compared to the deposited crystal structure, thereby exceeding the performance of the lignin force field for CHARMM. Additionally, LignAmb25 is shown to reliably estimate the enthalpy of vaporization and the absolute hydration free energy of lignin-related compounds. The LignAmb25 force field is provided in two variants: LignAmb25Solo, a standalone version not meant for use with other biomolecular force fields that focuses on accurate modelling of lignin solvent interactions, and LignAmb25HF, a version that is compatible with all other major biomolecular force fields in the AMBER molecular dynamics suite. This includes force fields of the GLYCAM (carbohydrates), ff19SB (proteins), and LIPID (lipids) families, as well as the DNA and RNA force fields routinely used in AMBER. The LignAmb25 force field will be distributed as of AMBER 26.