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Constraint generator

Submitted by Alison_Yajie on Wed, 2020-06-17 20:14
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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Rosetta 3 - Applications

Residue selector

Submitted by Alison_Yajie on Wed, 2020-06-17 19:57
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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Rosetta 3 - Applications

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

Submitted by nhinguyen26 on Wed, 2020-06-17 15:03
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? 

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Rosetta 3 - General

Segmentation Fault during prepacking

Submitted by Sunyp_IM on Fri, 2020-06-12 11:24
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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Rosetta 3 - Applications

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

Submitted by brspurri on Tue, 2020-05-26 08:12
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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Rosetta 3 - Applications

ligand_docking ligand preparation

Submitted by Alison_Yajie on Thu, 2020-05-21 10:21
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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Rosetta 3 - Applications

relax and movemap

Submitted by Alison_Yajie on Wed, 2020-05-20 21:27
Category: 
Docking

Can anyone suggest to me how to relax a protein with a non-covalent ligand? I want to make sure the ligand-binding site does not change dramatically.  In the following scenarios, which one looks reasonable:

1) relax protein with ligand; use movemap to exclude the rotamer of ligand residue 

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Rosetta 3 - Applications

Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1

Submitted by cm21 on Wed, 2020-05-20 08:55
Category: 
Docking
Design

Hi all,

I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:

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Rosetta 3 - Applications

RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

Submitted by brspurri on Thu, 2020-05-14 11:15
Category: 
Structure prediction
Docking

I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)

I am using the command: 

antibody_designer.macosclangrelease \
  -database /path/to/database/ \
  -do_dock \
  -use_epitope_constraints \
  -nstruct 5 -in:file:s complex_renumbered.pdb \
  -seq_design_cdrs H1 H2 H3 \
  -primary_cdrs H3 \
  -mintype relax \
  -run_snugdock \
  -run_relax \
  -out:path:all ./output

 

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