Generating CHARMM compatible force field parameters for atrazine

Abstract

There aremany synthetic, drug#likemoleculeswhose interactionswith large biomolecules
couldbepartlydescribedbymoleculardynamicsstudies.Theparametersnecessary toperform
anMDsimulationareavailableforbiomolecules(proteins,nucleicacids,lipids,carbohydrates)
and for many other small chemical compounds with biological relevance. In case of
uncharacterized molecules, parameter sets can be calculated using quantummechanical
calculations.
Theoptimizedgeometry,vanderWaals,charge,bond,angleand torsionparametersfor the
photosystem II#inhibitorherbicide,atrazine,werecalculated and integrated intoaCHARMM#
compatible parameter file. The file (.par) is available, along with the coordinates (.pdb),
structure (.psf) and topology (.top), andwith this four type of data, atrazinemay be part of
CHARMM#basedmoleculardynamicssimulations,therefore,itsinteractionswithbiomolecules
canbestudied.