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I'm not able to generate a score.sc file because something is not allowing me to dock my ligands to my protein. I get the error
Cannot normalize xyzVector of length() zero
Error: [ ERROR ]
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
Here's an example of my params file. I've attached a copy of my ligand/receptor .pdb and my dock.xml as well:
I can run rosetta docking protocol on my pdb file and there is no problem when I define partners as "MN_A". However, the same doesn't work on pyrosetta demo code of docking. I tried to solve this in several different ways by changing the docking jump value or etc but nothing acheived! Output models are still wrong in the format of M_NA. How can I fix this?
I am running snugdock locally for an Ag-Ab complex. Program is running fine but I am getting all score value 0.00.
SCORE: total_score rms CAPRI_rank Fnat I_sc Irms Irms_leg atom_pair_constraint cbeta cen_rms chainbreak complex_normalized dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA
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
The command I run:
rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params
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:
I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.
I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.
If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:
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.