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I am docking an antibody that has 20 residues in the H3 loop. I realize that this is a very challenging case. From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling. I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint. If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.
I am trying to use Rosetta surface_docking protocol to dock a 12 residues peptide on an ice slab.
I tried different formatting options of the input ice - peptide PDB file, but the software crashes.
After looking at the existing (Unsolved) posts on the forum, I created a PDB file formatted in this way:
Hi, I want to dock a protein to a TM protein embedded in a lipid bilayer.
Is there a way to do that with an implicit membrane model?
My current approach is to place explicit POPC lipids around the TM protein.
What would be the simplest way to make Rosetta being able to read the pdb file containing POPC?
Myself Haresh, I am postdoctoral fellow at University of Toronto. I used PyRosetta for protein protein docking and working good. Usually rosetta did protein protein doking between only two proteins. Is there any avaiblity or options to do protein-protein docking with bound ligand with each protein(e.g. Protein-Ligand --- Ligand-Protein)? Thanks in advance for your help.
Looking forward to hear from you.
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