Generating conformers on the B-ring of colchicine

User 40a6d33ef9

12-08-2010 22:54:13


I'm attempting to generate conformational isomers of colchicine (see attached file) with fluctuations in its B (middle) ring.

When I used the conformer generating tool (with various settings on the diversity limit), the conformations I got had no fluctuations in the conformation of the B-ring.

I'm wondering if there is a way in MarvinSketch to generate conformers with changes in the conformation of the B-ring, so that I can fully explore colchicine's ligand flexibility in docking studies.



ChemAxon 8b644e6bf4

19-08-2010 11:05:27

Dear Douglas,


Thanks for the question. We will need some more time to test if it is a bug or not (and in this case provide the parameters to use).

Sorry for the delay.




User 5fe8796231

24-08-2010 10:17:36



Interesting feature.

NHAc is axial in the attached sdf-file. However Clean3D and conformers plugin give only equatorial NHAc.

But only axial NHAc occurs for optical isomer (Clean2D & swap Up and Down bonds).