I think there is nothing incorrect in my command line to extract PDB files from a silent file:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:silent /mnt/hgfs/Downloads/silent.out -in:file:fullatom -in:file:silent_optH -out:output
The prompt goes well and completes successfully:
core.pack.dunbrack: Dunbrack 2010 library took 0.480358 seconds to load from binary
protocols.jd2.JobDistributor: protein_0001_0001 reported success in 3 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds
However, there is no any PDB files in /mnt/hgfs/Downloads. Only a file of score.sc is created.
It still remains the same though "-out:path:all -out:path:all" is added.
Can I ask how to get the PDB file?
Thank you very much.