I have a multi-ligand file, NBU_confs.pdb, of ligand conformers (291 total) and the line "PDB_ROTAMERS NBU_confs.pdb" at the end of the params file, and the pdb (coordinates) of one of the ligand conformers at the end of the input receptor file for docking. My questions:
1. Does Rosetta use the other conformers in NBU_confs.pdb. If so why does it need to have the pdb of just one conformer at the
end of the input receptor file?
2. If I run on several CPUs, each with -nstruct 1000, using the same input receptor file, params, options etc..., would the
run on the second, third, forth etc... processor just be repeating the run on the first one or it's a random process and
thus the decoys from all the runs will be different? Would it be better to split NBU_confs.pdb into different smaller files
and use each individually for each run?
3. Is it advisable to dock to a rigid receptor with Rosetta? Could you point to a options or xml files for this?