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I have a protein sequence that consists of two domains: A and B. The two domains presumably interact and there are some residue pairs that can be used as constraints. However, I don't know whether these domains interact within a single protein (A-B) or a dimer (A-B', B-A'). Given the fact that both A and B have many good templates in PDB, I thought that Rosetta comparative modeling protocol could be used to investigate these two scenarios. I would appreciate suggestions on how to set up such an analysis.
I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump.
I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.
I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.
I have written a script using PyRosetta (pyrosetta-4.0-py2.7 retrieved from github 2017-05-23) which:
- imports a PDB file containing a full antibody structure and antigen dimer separated by around 100A
- defines a custom fold tree with the Fc at the root and a jump edge connecting the Fc to the antigen
- creates ambiguous site constraints consistent with interaction of variable loops of the two Fab domains with the epitope of each antigen in the dimer
Dear Rosetta community,
I am looking for a reason why my simulations stop before -nstruct is reached. This happens when I use rosettascripts.mpi.linuxgccrelease for some flexible docking. As many decoys don’t pass the Rosetta filters, I set -ntrials to 100.
And then, with:
I get exactly 500 decoys (which I anticipate), but for:
-nstruct 30 000
during I'm using flexpepedock, I gengerated a param file for the ATP. But in the prepack step, the program moved my ATP out of the ATP pocket. I've used movemap and constraint file but it didn't work. The ATP still got "kick out".
I was wondering how to let ATP not move during the prepack step?
I attached the PDBs before and after prepack step as well as my prepack flags.
I'm doing docking peptides to kinase structure by using flexpepdock. In the meanwhile I need ATP in the kinase structure, therefore I generated a param file for ATP. But after the prepack mode, the ATP has been removed from the pocket to the somewhere in the structure. Here is my question:
1) how should I fix the ATP in the pocket without any movement? Movemap or constrain file?
2)I was told to use movemap to fix the ATP. But I don't know how's the rosetta numbering of the HETATM.
Using placestub application, I want to place a set of stubs in target protein to use them for protein binder design. In this way, I want use 1000 scaffold (proteins to be substituted by appropriate stubs). Everything is OK with producing stubs, inverse rotamers, docking. But when I run placestub xml, it gives me this type of error in last line: