Weird Ligprep error / simple workaround

I have prepared an sdf using an Openeye software. The sdf is imported into KNIME and processed shown in the workflow picture. The Ligprep nodes are identical, and produce (as far as I can see) identical log files.

The error message shown when hovering over the (X) is:
Execute failed: Null

Anyone got an idea what's wrong?

What version of the Schrodinger plugin are you using? Also, what does the log file look like? Did Ligprep run? Are there files in your schrodinger temporary directory? (i.e., the directory that is set under Preferences -> Knime -> Schrodinger -> "Directory for temporary files")?


Schrödinger extensions 1.1

The ligprep log files look good. As I mentioned the two log files from ligprep are almost identical in the case were it works and when it does not.

When looking at the problem a little more I see that the ligprep node does not seem to be able do work with sdf:s if the "include input" or "match input" boxes are checked in the ligprep node.

The version is shown in the $SCHRODINGER/knime-v*/ (where * is the version number). I am glad you have found a workaround. We have changed the Include Input parameter in Ligprep (and other nodes) to "Output Column Structure" which allows you to specify the output (i.e., Input plus Output, Output replaced within Input columns, or Output only). Together with the Match Input option, these options make it a bit easier to understand what to expect in the output columns.

If you do want to use the Input data in your current version, you can use the "Lookup and Add Columns" node to do so.

Hope this helps.


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