Protein descriptors in knime using chemistry external tool


I’m implementing a knime workflow to calculate protein descriptors of a protein by inputing its fasta sequence. I tried using the chemistry external tool node to calculate these features as outlined in this workflow:

But, I don’t get any features as any output but rather an empty column saying text and it’s splitting my fasta input into name (string) and sequence(Seq). Can someone help me on what am I doing wrong here?

Hi @hrshita -

Since this question is specific to the @Schroedinger extension, I moved it to the appropriate forum category. Now that I have tagged them, maybe they can jump in to provide additional assistance. (Also maybe @Alice_Krebs may know?)


Sorry to hear that you run into problem when trying to calculate the sequence based descriptors using the script.
Can I please check with you which version of the Schrodinger suite you are using?
A quick test to check the problem further would be to run the script outside of Knime using:


command to see if this will show the help text and you can then use this specify the input sequence and see if the calculation would work ok?

If the problem still remains, please send us the details you see in command line or from the Console view from Knime and we will be able to help you further with this.
If possible, please reach out to directly and we will be able to help you further this way as well.

Many thanks,


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