Problems with optional parameters of Openbabel node


I found a strange behavior while using Openbabel node that could represent a bug. I'm trying to convert an sdf molecule to a mol2 one using MMFF94 atomic charges. This type of charges is not the default one and to calculate it through the standalone Openbabel version the parameter “--partialcharge mmff94” must be added from the command line, after the input file specification.

In Openbabel KNIME node configuration window there is a field called “optional parameters” that in principle is designed exactly to pass non-default, optional parameters to Openbabel. As you can see in the attached workflow using the Openbabel KNIME node, neither if I use the bundled version nor the external version of Openbabel, I do not obtain the desired MMFF94 atom charges. Instead of those, the default “gasteiger” charges are calculated (as shown in the 5th row of the mol2 file).

Nevertheless if I run the external version of Openbabel from the External Tool (Labs) node I do obtain the desired MMFF94 charges.

Is this a bug? Maybe also this thread can be related with this problem. I'm using the last current version of "KNIME Base Chemistry Types & Nodes" (3.2.2.v201609201941)


Hello Gio,

Thank you for reporting this. We will have a look into it and report back to you.



Thank you Ferry

This will be fixed in 3.3.2.

Very good Wiswedel, thank you to report this to this forum thread.