Abinitio is one of those applications still on the old job distributor scheme, rather than the “jd2” setup. As such it has very limited options for input and output. One of those limitations is that it only outputs silent files, and doesn’t obey flags for PDB output. This isn’t much of a limitation in practice, as for most ab initio runs you need to run a *large* number of output structures, so probably should be using silent file output anyway. Once you’ve identified the structures you want as PDBs, you can extract those few structures with the extract_pdb application (extract_pdbs.linuxgccrelease -in:file:silent silent.out -tags [list of tags to extract])
I don’t quite understand what you mean by “incomplete” – could you elaborate?
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