I am using this following code
babel -i sdf *.sdf -o pdb > *.pdb --gen3D
I got warnings like 3D coordinate generation failed
Errors/Warnings
*** Open Babel Warning in CorrectStereoAtoms Could not correct 3 stereocenter(s) in this molecule () with Atom Ids as follows: 13 18 20 Warning: Stereochemistry is wrong, using the distance geometry method instead
Hi Debanjan,
You should begin to check the chemical structures in your SDF file.
And try the following command line:
babel -isdf xxx.sdf -opdb xxx.pdb --gen3d
Thanks for the reply, Yoshinobu Ishikawa.
But what should I check in the SDF file to correct the error? Can you put some suggestions into it.
You can check your SDF files by SDF viewers or chemical drawing softwares like ChemDraw.
Prior to converting to 3D models, you should re-format your SDF file using Open Babel like:
babel -isdf xxx.sdf -osdf xxx_ob.sdf
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