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Dear friends,
After using a PDB of -740 REU to run ddg_monomer, I use score_jd2.linuxgccrelease to score the silent output. In the score file (attached), the first two elements are "total_score" and "score". The scale of "total_score" is close to the talaris2013, i.e. -700 to -730; the scale of "score" is -1000, much lower than -700.

Can I ask
1) What is the difference of "total score" and "score"?

2) Why cannot we just use one score?

Dear friends,
I was using relax.linuxgccrelease to relax my protein (442 residues) with 100 outputs:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/relax.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -s /home/lanselibai/Cheng/relax/input/C226S_raw.pdb -out:show_accessed_options -nstruct 100 -relax:quick &> /home/lanselibai/Cheng/relax/output/record.log &

Then I score it using score_jd2.linuxgccrelease:

Hello everybody,

i have done structure calculation of a protein with four zinc atoms. I have a native structure and i want to refine this structure. In every calculation I found the following error:

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.