You are here
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.
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?
I am using "local refinement" to calculate the I_sc of protein complexes. When I ran Rosetta for the exact same structure multiple times and I got a significant fluctuation in I_SC score, ranging from -2 to -15. This means that in one trial, the complex is unfavorable, but it is favorable in the subsequent trial. What is the reason for this? How can I overcome it?
Thank you in advance,
I am attempting to dock a peptide onto a protein using flexpepdock. The docking completes and the identified structures are plausible solutions. However, when I examine the score.sc file, I notice that the I_hb term has a single, extremely high value for all structures:
I_hb = 18446744073709551616.000
I am prepacking the structure before docking:
FLEXPEP -s PEPTIDE.pdb -flexpep_prepack -ex1 -ex2aro -overwrite
FLEXPEP -s PEPTIDE_0001.pdb -pep_refine -ex1 -ex2aro -nstruct 100 -lowres_preoptimize -native PEPTIDE_0001.pdb
I am starting to learn Rosetta right now and have to relax a structure before I learn more because of a deadline.
After I run the Rosetta Relax successfully when I load the result in Chimera, the pdb seems to be off from the density by a little bit. But when I fit it in, it looks better.
Is this normal? Or am I doing something wrong?
(My structure has multiple repeats of the same unit and I am only fitting one of them)