Hi Vineet, I did not used JLIGAND so far, so I cannot explain what happend, but maybe the quickest solution would be a manual intervention in the cif-files. Type at at the chirality remark "positiv or negativ" or whatever nomenclature is used and save it again. I do it sometimes for my ligands when I genereated the wrong stereoisomer or the description for the racemate.
Good Luck Christian Am Donnerstag 21 Juli 2011 23:10:01 schrieb Vineet Gaur: > 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 >
