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RDKit calculate charge node

Member for

2 years 4 months Bboe

Hi everyone,

I have a problem using the 'RDKit calculate charge' node.

What I have : A file containing 2 columns : Canonical Smiles + Inchi Key

What I want : Convert SMILES into SDF file with gasteiger charges.

What I do : I use the 'molconvert' node to convert SMILES into SDF then the 'RDKit calculate charge' node to calculate the charges.

What is the problem : For some of the molecules I have the following error :

"ERROR RDKit Calculate Charges 4:16       Failed to convert cell SDF Parsing Error (MolSanitizeException) for MoleculeX"
"WARN  RDKit Calculate Charges 4:16       Empty cell in ('SDF', 'Row436544'). All result cells will be empty."

But I have not any empty cell when I look at the file. 

Is there any solution to this or this is a problem that can not be avoid ?

Thank you for your answer

Best wishes


Thu, 02/22/2018 - 11:27

Member for

12 years 7 months



The error/warning messages you are describing are typically due to molecules that have atoms with unrealistic valences, but it's tough to tell from the information provided so far.

I'm not 100% sure what format you would like to have in the output SDF, but the attached workflow shows a relatively simple way to, starting from SMILES, generate an SDF that includes a "charges" data field for each molecule.

I hope this helps,


Wed, 02/28/2018 - 02:53

Member for

2 years 4 months


Hi Greg,

Thank you for your answer, the workflow you sent me work perfectly for what i want to do.

have a good day