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Docking

select_best_unique_ligand_poses - Ligand docking

Category: 
Docking

Hi There,

I performed the ligand docking protocol with 250K sampling. I would like to use the 'select_best_unique_ligand_poses' application to find the unique binding modes. However, the run gets crashed with an MPI error: killed with signal 9.  I thought this is something related to the memory, so I tried using nodes with higher memory, such as 125GB and 500GB, but still, I get the same error. 

Can somebody suggest me a workaround for this?

Thanks,

Subha

Post Situation: 

FlexPepDock Multi chain receptor

Category: 
Docking

Hello,

I am docking a pep to a receptor with two chain, using FlexPepDock ab initio. Both the chains are number starting with 1

In the flag file, I set -flexPepDocking:receptor_chain A,B

However, it ouput the errors such as

protocols.TrialMover: Acceptance rate: 0.02

core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-1, 556-2, 556-3, 557-1!

core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-2, 556-3, 557-1, 557-2!

Post Situation: 

splitfile.py

Category: 
Docking
Small Molecules

I'm looking at the methods of the following paper:

Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.

and trying to follow along (to eventually adapt it for my own work).

I've hit a snag at one of the commands:

Post Situation: 

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: 

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