Docking

What is the best way to define a custom fold tree?
I find that -auto_setup_metals does not work for me and I'd like to set up my fold tree manually.

Thanks!

docking_prepack_protocol generates several output pdb structures:

away__*_0001.pdb
away_packed__*_0001.pdb
initial__*_0001.pdb
prepack__*_0001.pdb
*_0001.pdb

where * stands for the name of the crystal structure that was given as input to docking_prepack_protocol.

What are the differences between these .pdb files that docking_prepack_protocol outputs?

Hello,
I would like to know how to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches?
In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other new linear peptide structures at this same binding site, in order to run the docking calculations using the rosetta3 protocols.

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.