Structure of a lignin peroxidase ligand access channel-atrazine complex after molecular dynamics simulation

Published: 15 April 2018| Version 2 | DOI: 10.17632/b2wn6fdcj4.2
Contributors:
János Ecker,
László Fülöp

Description

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.

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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)