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Article ID: 1573 - Last Modified:

My IFD job dies in the Prime stage with the error

"ERROR: Unable to read options from top-level input file"

What's wrong?

This error is typically seen when a ligand file in SDF format is used in IFD. Although allowed by the GUI, the Prime executable is not able to correctly parse a ligand file in SDF format. The solution is to convert the ligand file to Maestro format and use the converted file as input.

You can convert the SDF ligand file by reading it into Maestro and then exporting in Maestro format, or, if you prefer to use the command line, there are two utility scripts you can use:

$SCHRODINGER/utilities/structconvert

and

$SCHRODINGER/utilities/sdconvert

that will do the conversion for you. Run the scripts with -h to see usage and options.

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