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?

Vineet Gaur

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