Dear all, I am trying to generate a cif file for a new ligand (a sugar derivative) using "JLigand". The ligand needs to be in D- configuration. However, after I input the coordinates for this ligand into J ligand and carry out geometry regularisation, the program automatically converts D configuration to L. Had anyone encountered similar kind of problem while working with JLigand and how can I tackle this issue?
I am using JLigand since I have to define a covalent link between the ligand and the mocromolecule later during the refinement. Is there any other program other than Jligand (or Prodrg server) which I can use for generating the cif file and defining the link? Thanks, Vineet Gaur