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Docking

proteins.pdb: Not enough chains in submitted protein! [At least 2 chains should be present, found chains: [u'A']...]

Category: 
Docking

Hello,

 

I am trying to dock two proteins but I keep getting this error. I am not sure why its there as there are two chains in the pdb.

Can anyone help?

Thank you

Post Situation: 

Error when run script "thread_pdb_from_alignment.py"

Category: 
Docking

Hello guys,

I'm using the ligand docking protocol, and when I put the command below it does not generate the expected output file "2ou0_threaded.pdb"

command:

/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py --template=2anv_A --target=2ou0_ --chain=A --align_format=clustal alignment.aln 2anv_A.pdb 2ou0_threaded.pdbD

Error:

Post Situation: 

comparative modelling of a complex

Category: 
Structure prediction
Docking
Constraints

Hello All,

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.

Best wishes,

Post Situation: 

What is the expected behaviour when minimizing a jump edge?

Category: 
Docking
Constraints
PyRosetta

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.  

Post Situation: 

Minimization not changing jump edge vector length

Category: 
Docking

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

Post Situation: 

jd2 quits before reaching -nstruct # in roseta_scripts.mpi.linuxgccrelease

Category: 
Docking

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:

-nstruct 500

-ntrials 100

I get exactly 500 decoys (which I anticipate), but for:

-nstruct 30 000

-ntrials 100

Post Situation: 

Method to keep ATP in the certain position in the prepack step

Category: 
Docking

Dear all,

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.

Thank you!

Post Situation: 

how to fix the ATP HETATM by using movemap or constraint file?

Category: 
Docking

Dear all,

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. 

Post Situation: 

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