Docking

Hello,

I'm trying to use the highres docking protocol  with rosetta3.9 and I still get this error (see below), no matter what I do with the xml protocol (attached):

I would appreciate any suggestion
best regards,
Dave

The command I run:
rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params

Hi,

I am trying to dock a peptide into a protein with rosetta. My peptide and protein have capping groups (ACE, NMA), which are recognized by the relax protocol and incorporated into the terminal residues. I then put the relaxed structures together into a complex.pdb file and tried to run the docking protocol:

Hello,

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

Dear Rosetta Team,

When docking a protein with a solid surface, Rosetta will need a .surf file; Any one can tell me how to setup/edit a .surf file for a certain solid surface (a .pdb file) for surface docking? In the demo example for the calcite.surf, there is not detailed instruction to tell how to do it? Only three lines, with likely X,y,z in the calcite.surf file. I dont know what they are representing for a solid surface?

Thanks

An Pu