haha, i totally agree on that.!
This is one of the options in the flag for ligand docking:
-out
## These channels generate a LOT of output,
## especially with -improve_orientation.
-mute protocols.geometry.RB_geometry core.scoring.dunbrack.SingleLigandRotamerLibrary core.scoring.rms_util
## Number of trajectories to run (per input structure given with -s)
-nstruct 500
## With multiple processes, ensures a unique name for every output structure.
## Each process should get a different string here, so you can’t really
## put it in the FLAGS.txt file, it has to go in the Condor script:
#-suffix 3
-file
## I prefer output structures with Rosetta numbering, from 1 to N residues.
## To keep the original PDB numbering, omit this flag:
-renumber_pdb
-path
## Where to write the silent.out file. Specified in my Condor script.
#-pdb work/jnk_pp_1_001/3
So, I don’t think I can change it to output as pdb files instead. And using the extract_pdbs.linuxgccrelease, it says “bad format in first line of silent file”, then the process stopped after a while, not generating any pdb files. What can I do to resolve any of these issues? 
In addition, is there any difference in using extract_pdbs or extract_atomtree_diffs.linuxgccrelease? Also, I encountered a ‘unrecognized aa 100’ error when using ligand_rpkmin.linuxgccrelease, what does it mean?