Structure of a lignin peroxidase ligand access channel-atrazine complex after molecular dynamics simulation
Published: 26 September 2017| Version 1 | DOI: 10.17632/b2wn6fdcj4.1
Contributors:
János Ecker, Description
State and contacts of the lignin peroxidase ligand access channel-atrazine complex after 5 ns molecular dynamics. The simulation was performed with NAMD (CHARMM36 force field). The input structure for the simulation was created by molecular docking. See: http://dx.doi.org/10.17632/dvjms8448j.1
Files
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.1 2. Save the file as a protein-ligand complex with AutoDockTools. 3. Energy minimization with NAMD (20-30 ps). 4. Molecular dynamics with NAMD: solvation and neutralization, 5 ns, NPT microcanonical ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field.
Institutions
Szent Istvan Egyetem Mezogazdasag- es Kornyezettudomanyi Kar
Categories
Three-Dimensional Graphics, Enzyme Structure, Enzyme Structure-Function Relationship, Ligand Binding, Three-Dimensional Reconstruction of Biomoleculair Structures