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.