INTRODUCTION: This script was part of the Ph.D. project where we constructed MOFs consisting of Metallic (Fe, Ru, Cu) ions coordinated with bipyridine molecules. This technical construction consists of first creating the main unit fully optimized with DFT in the gas phase and getting the corresponding NBO or Mulliken charges. The next phase is to repeat this unit in all three directions with the same corresponding charges of the main unit. Overall, this is the assumption where we have assumed that the system is homogenous, the electrostatic field is the same everywhere. Now, we have to fix the boundary points. This, however, is a difficult problem because the truncated charges have to be taken into account. This is explained in the thesis.
This complex construction was part of a PhD thesis in which we devise a method to construct Fe(bpy) based MOFs. It uses python libraries. The Amber FF parameters were fitted to DFT calculations. Click this link to get to HAL archive!