I am new to Rosetta. And we hope to redesign a protein and let it easier to dock with another two protiens. Hope to verify if my approach is correct here.
Step 1) I applied the Rosetta protocol - remodel and create the blueprint file by "~/rosetta/main/tools/remodel/getBluePrintFromCoords.pl"
Step 2) Edit the blueprint file and apply the commands ALLAAxc to all residues.
Step 3) run the remodel with my pdb file and chain code input by "~/rosetta/main/source/bin/remodel.linuxgccrelease -database ~/rosetta/main/database -s <pdbfile> -run::chain <chain> -remodel:blueprint <blueprintfile> -overwrite"
Step 4) It generated the xxxx0001.pdf file which is said the best one and it also has .sc score file. Moreover, other 5 pdb are created while it is said the 1.pdb is the same as the xxxx0001.pdb.
Now I have some questions :
Q1) When I put the ALLAA in the first two residues position, I got error "File: src/core/pack/task/ResfileReader.cc:1577 On line 3, the pose does not have residue with chain=D, PDBnum=1." The log file is attached. However, when I left the first two residues empty and apply ALLAA to all the other residues, it will not have error and Step 4) can be achieved. How is that reason ?
Q2) Can I fully trust the xxxx0001.pdf file is the best score one ? Then go to the lab for further testiing. Should I apply docking protocol to compare it with the other 4 pdb mentioned ?