[ccp4bb] JLigand: Handedness related issue

[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

[ccp4bb] JLigand: Handedness related issue

[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

Re: [ccp4bb] JLigand: Handedness related issue

[Christian Roth]

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