Docking

Hello, I am using rosetta docking_protocol compiled with Intel MPI (from Intel® oneAPI Toolkits 2020), and I have some problems / bug reports.

I requested 3 output poses with '-nstruct 3' and I ran 'mpirun -n 3 docking_protocol.mpi.linuxiccrelease ...' to start one master rank and two slave ranks. However, when one slave (rank 2) finished its jobs and master will send spin down signal:

Hello Rosetta people,

I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.

How many rifdock can I run at a time on a 64 CPUs and 512GB memory server?

I tried 8 rif_dock_test running at a time, but I lost connection with my server several hours later(maybe 5 or 6 hours). My guess is the server was overloaded, so that the connection was lost. 

I used uptime command to check out, the system load is nearly 800%, does that mean I can only run one rif_dock at a time?

I am trying to validate a .xml script to be used by rosetta_script application. I copied the .xml file from the paper:  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein−Ligand Docking. But the valdation fails...

When I run,

validate_rosetta_script.default.linuxgccrelease -parser:protocol crystdock.xml -parser:script_vars sg=input random=0

Here is my XML: