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"

<p>This dataset accompanies the manuscript: " <i>Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH∙∙∙Nucleophile in Transition State Stabilization in Arabidopsise thaliana Cell Wall Invertase 1</i>".</p><p><br></p><p>It contains sample CHARMM input and output files, topologies, and parameters required for QM/MM calculations of reaction in a plant cell-wall invertase.</p><p><br></p><p><b>The QM/MM inputs include:</b></p><p>1. QM/MM MD simulation</p><p>2. Energy minimization</p><p>3. Reaction path calculation (adiabatic mapping)</p><p>4. Umbrella sampling MD along reaction coordinate (PMF computations)</p><p><br></p><p><b>The outputs from QM/MM umbrella sampling MD include:</b></p><ul><li>Snapshots of stationary points on the PMF plots in Figure 3A for sucrose hydrolysis catalyzed by a plant cell-wall invertase 1 from <i>Arabidopsise thaliana </i>(see Figure 3 in the main text, DOI: 10.1021/acs.jcim.3c00796)</li><li>Trajectories from the last 40 ps of 100-ps umbrella sampling simulations</li></ul><p><br></p><p><br></p><p><br></p><p><br></p><p><br></p><p><br></p><p><br></p><p><br></p>