I am trying to run the Protein Preparation Wizard from the command line with -NJOBS for multicore processing but I am getting this error message:

PDB format is not supported for StructureWriter
RuntimeError: PDB format is not supported for StructureWriter

What is the problem?

It looks like you had the output file format set to PDB (filename.pdb). For multi-structure processing, you will have to set the output format to Maestro (filename.mae), as multi-structure PDB files are not supported.

The -NJOBS option is used to distribute the preparation of multiple proteins. The input file must be a multi-structure Maestro file. So, as an example, if you had a Maestro file with 3 proteins (3_pdb.mae) to be prepared, you could run a command like this:

$SCHRODINGER/utilities/prepwizard -NJOBS 3 -HOST MY_HOST:3 3_pdb.mae 3_pdb_prep.mae

in order to distribute the job over three processors on MY_HOST.

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