Scope of Molecular Dynamics Simulation to fit difference X-ray Solution Scattering Curves


To explore the scope of Molecular Dynamics Simulation for fitting difference X-ray Solution Scattering Curve

  • Parametrization and input file preparation of the Heme cofactor is done with 'ANTECHAMBER', 'PARMCHK' and 'LEAP'
  • Molecular dynamics Protocol involves Molecular Mechanics Minimization, Heating, Equilibration and Production steps.
  • After equilibration, in-house Perl codes are used for automating the production run with 'SANDER' and simultaneously calculating the X-ray solution scattering curves with CRYSOL following every iteration.
  • Difference curves are calcualted from the coordinates geneated from molecular dynamics simulations and compared with experimental data with chi-square.