Generating conformers on the B-ring of colchicine

Hi,

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.

Thanks,

Douglas

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.

 

Regards,

Gabor

Hi

 

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).

 

Alexandr