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
>
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