Docking

Hello, 

I'm attempting to compare protein-protein docking at pH 7 / 11. I've protonated my structures using PROPKA and have performed pre-packing and docking using the following commands:

docking_prepack_protocol.static.linuxgccrelease -database /apps/local/biology/rosetta/2020.11/bundle/rosetta_bin_linux_2020.11.61179_bundle/main/database/ -in:file:s model_5.pdb -unboundrot unbound_rotamers.pdb -nstruct 25 -partners A_B -ex1 -ex2aro

Hello,

I am attempting to use the GALigandDock mover to perform dockings of a metal ligand similar to heme. I am following this paper: https://pubs.acs.org/doi/suppl/10.1021/jacs.3c02742/suppl_file/ja3c02742_si_001.pdf.

I generated a params file using the molfile_to_params script, and proceeded to use the exact same command and docking xml file.

Hi, everyone:

    I want to generate pos file for different scaffolds, and I find that gen_apo_grid can satisfy my needs. But there is a problem, if this option "-packstat:surface_accessibility"  is on, I can set the value of "-packstat:min_surface_accessibility". Whatever value I set for "-packstat:min_surface_accessibility", the output pos file does not change at all. 

Example Command Lines: 

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: