I am using the flags for the low resolution protocol as documented here (https://www.rosettacommons.org/docs/latest/ddg-monomer.html):
-in:file:s <pdbfile of the preminimized wildtype structure> # the PDB file of the structure on which point mutations should be made
-ddg::mut_file <mutfile> # the list of point mutations to consider in this run
-ddg:weight_file soft_rep_design # Use soft-repulsive weight set
-database /path/to/rosetta_database #the full oath to the database is required
-fa_max_dis 9.0 # optional -- if not given, the default value of 9.0 Angstroms is used.
-ddg::iterations 50 # 50 is the recommended number of iterations
-ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration
-ignore_unrecognized_res # optional -- if there are residues in the input PDB file that Rosetta cannot recognize, ignore them instead of quitting with an error message
-ddg::local_opt_only true # repack the residues in an 8 Angstrom shell around the site of the point mutation
-ddg::suppress_checkpointing true # don't checkpoint
-in::file::fullatom # read the input PDB file as a fullatom structure
-ddg::mean true # do not report the mean energy
-ddg::min false # report the minimum energy
-mute all # optional -- silence all of the log-file / stdout output generated by this protocol
-ddg::output_silent true # write output to a silent file
To these I added the flag: -out:path:all "path/to/dir", since I wanted all the minimized .pdb structures to go to one specific destination folder.
For some reason this isn't working as expected. All I am getting is a wt_K30E.out and a mut_K30E.out files, instead of the 100 (50 for wt and 50 for mut) structure files I expected. What am I doing wrong?
You used the option "-ddg::output_silent true". This means that you requested the application output the structures in "silent file" format (one file with multiple structures), rather than as individual PDBs.
I tried setting "-ddg::output_silent false" and omitting the option "-ddg::output_silent", but I am still getting the silent .out files, instead of .pdb files. What could I be missing?
When I use "-ddg::output_silent false", I can get PDB.
Another way of doing that is: convert the silent file into PDB afterwards. e.g.
~/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/silent1.out -in:file:fullatom -in:file:silent_optH -out:pdb
Thanks. I ended up using extract_pdb. I should mention I am using v3.5.