Structure of a lignin peroxidase ligand access channel-atrazine complex after molecular dynamics simulation
State and contacts of the lignin peroxidase ligand access channel-atrazine complex after 5 ns molecular dynamics simulation. The simulation was performed with Nanoscale Molecular Dynamics (NAMD) application (CHARMM36 force field). The input structure for the simulation was created by molecular docking.
Steps to reproduce
1. Docking of atrazine to the lignin peroxidase ligand access channel's surface. More details: http://dx.doi.org/10.17632/dvjms8448j.2 2. Save the docking output file as a protein-ligand complex with AutoDockTools. 3. Energy minimization with NAMD (20-30 ps). 4. Molecular dynamics with NAMD: solvation and neutralization, NPT microcanonical ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field, Duration: 5 ns. The CHARMM-compatible parameters of atrazine can be obtained by quantum chemical calculations. Parameterized structure of atrazine is available: http://juso.hu/index.php/JUSO/article/view/8 (Ecker, J. J. Univ. Sci. 3, 1-8, 2016)