Aromatic cycles with molconvert

Hi,

I would like to know why molconvert removes aromatic cycles when I transform my ligand from PDB to SDF?

My command is: molconvert sdf ligand.pdb -o ligand.sdf

Thank you.

Dhoha

Hi,

 

The pdb format does not store the bond types, only the atomic locations.

The bond types are guessed from the atomic distances. This calculation is not perfect and never can be.

Unfortunately, you will have to correct the structures manually.

 

BRs,

Peter