Sample QM/MM files for "Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH∙∙∙Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell Wall Invertase 1"

This dataset accompanies the manuscript: " Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH∙∙∙Nucleophile in Transition State Stabilization in Arabidopsise thaliana Cell Wall Invertase 1".

It contains sample CHARMM input and output files, topologies, and parameters required for QM/MM calculations of reaction in a plant cell-wall invertase.

The QM/MM inputs include:

1. QM/MM MD simulation

2. Energy minimization

3. Reaction path calculation (adiabatic mapping)

4. Umbrella sampling MD along reaction coordinate (PMF computations)

The outputs from QM/MM umbrella sampling MD include:

• Snapshots of stationary points on the PMF plots in Figure 3A for sucrose hydrolysis catalyzed by a plant cell-wall invertase 1 from Arabidopsise thaliana (see Figure 3 in the main text, DOI: 10.1021/acs.jcim.3c00796)
• Trajectories from the last 40 ps of 100-ps umbrella sampling simulations