One option is to store things in silent files, rather than as PDBs. You can do this by adding the option `-ddg:output_silent` to the command line, and set the filename for the silent output with the -out:file:silent option.
This will allow the ddg_monomer application to work, but you’ll likely run into issues when extracting the PDBs at least if you do it in the standard fashion with the extract_pdbs application. Luckily, though, you should be able to use a text processor (such as sed) to change the tags in the silent file from their long and unwieldy versions to a version which is easier for you to handle. You can then pass that edited file to -in:file:silent for extract_pdbs to get PDB files with filesystem friendly names.
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