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Docking

How to create a native file for Protein-Protein docking

Category: 
Docking

Hi,

 

We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.

 

 

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How to select docked models

Category: 
Docking

Dear all, 

I have generated 500 docked complex model with docking_protocol.linuxgccrelease using a command like this:

docking_protocol.linuxgccrelease\
  -s start_prepacked.pdb\
  -partners A_B\
  -dock_pert 3 8\
  -ensemble1 prot1_ensemble.list\
  -ensemble2 prot2_ensemble.list\
  -out:path:all docking\
  -nstruct 500 | tee docking.log

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How to create a native file for Protein-Protein docking

Category: 
Docking

Hi,

 

We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.

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error when using script best_ifaceE.py

Category: 
Docking

Hi I have output my ligand-docked pdbs in silent out as both pdbs and in binary but regardless when I run the script to identify the top 10 percent based on IF delta score I get the following error.

 

FILE]: src/protocols/jd2/AtomTreeDiffJobInputter.cc

[LINE]: 132

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: No valid input structures found for AtomTreeDiff file.

 

 

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

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Constraint generator

Category: 
Docking

 

Question on using HydrogenBondConstraintGenerator

 

The score function I am using is ref2015.wts. It is said that to apply constraint properly, the scorefunction being used needs to have a non-zero weight for the appropriate constraint score term. Does that mean I need to add coorndinate_constraint, atom_pair_constraint or/and angel_constraint into ref2015?

 

If I want to apply for constraint while docking, but want the original score (without constraint) to be displayed. Do I set mover like this?

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Residue selector

Category: 
Docking

Question on residue selector: If I have chain A and chain B. Chain A having residue 1-20 and chain B has residues 1-20. If I want to select residue 1-10 from chain A. Does the following script correct? Or I have to name residue in Chain B as 21-40 to distinguish them from residues in chain A

<RESIDUE_SELECTORS>
     <Chain name="chA" chains="A"/>
     <Index name="res1to10" resnums="1-10"/>
  </RESIDUE_SELECTORS>

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Ligand docking: how to generate the crystal_complex.pdb with hydrogens added

Category: 
Docking

Hello,

I'm having trouble with how to generate the crystal_complex.pdb with the ligand hydrogens added. I have tried cleaning the pdb while keeping the ligand with the clean_pdb_keep_ligand.py script but the ligand in reported crystal structure has no hydrogens. Using that crystal_complex.pdb for docking study gives error: " The native pose passed to InterfaceScorecalculator does not have chain X. " Is there a way we can clean the pdb, keep ligand, and add the hydrogens? 

Post Situation: 

Segmentation Fault during prepacking

Category: 
Docking

Dear all,

   When I do prepack of a antibody-antigen complex with the following command,

mpirun -np 6 docking_prepack_protocol.mpi.linuxgccrelease\
  -in:file:s nb0-ag-start.pdb\
  -ex1\
  -ex2\
  -partners H_A\
  -ensemble1 nb_ensemble.list\
  -ensemble2 ag_ensemble.list\
  -docking:dock_rtmin\
  -out:path:all prepacking
 

I always get a "segmentation Fault" like the following: 

[END_BACKTRACE]

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RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category: 
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb. 

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

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ligand_docking ligand preparation

Category: 
Docking

Can everyone tell me why my ligand FMN is twisted after using molfile_to_params.py script to prepare param file? It still looks normal when I open with pymol. But it looks twisted after I open with Maestro. 

Does anyone have similar experiences? 

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