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Docking

Prepacking crashing using metalloprotein

Category: 
Docking

Good evening, 

I'm trying to run an ensemble protein-protein docking to a protein containing a metal cluster (2Fe2S). I was able to generate ensembles for both structures, but at the Prepcking stage the application just crash. Here is the command:

$ docking_prepack_protocol.default.linuxgccrelease -in:file:s ../input/mnt_bcl2_relaxed.pdb -ensemble1 ../ensemble/mnt/mnt_A_ensemblelist -ensemble2 ../ensemble/bcl2/bcl2_B_ensemblelist -partners A_B -in:auto_setup_metals true @prepack_flag

Here is the error message:

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Help to understand docking results

Category: 
Docking

Dear colleagues, everything's ok?

I have done a docking experiments between enzyme and inhibitor.

I did global docking on cluspro web serve, following did a local and refine docking procedure.

Wight parameters, I should look to compare the docking results with my kinetics data

total score X rms; I_sc X Irms or something else?

I ask for help because some results appear so artificial.

Thanks any way

Ricardo

 

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RosettaDock output

Category: 
Docking

Hi, now Iam havin gsome trouble about the RosettaDock app.

Few months ago when I proceeded the docking app, I got about 1,000 model resuts as output.

Now I get only 1 model output even though I used same input model and protocol.

Anyone can help me or having same problem with me?

Thank you!

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Rosettadock Error

Category: 
Docking

Hi,

I tried to dock a ligand protein to a receptor (a dimer) by using the rosettadock websever, but unfortunately it failed. I did not get the docked conformations. My job id is 4910. In the 2.docking.output.0 file, there is the error message:

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snugdock: constrained backbone

Category: 
Docking

Hi,

I am running snugdock for Antigen-Antibody docking. As I can see from the output pdb files, the loops are moving during docking.  After reading snugdock paper I do see the reason for that.

But in my case, I would like to fix the backbone of both Antigen and Antibody (for loops and nonloop regions). 

I tried to include "-relax:bb_move false" flag, but it seems like it is doing nothing.

does anyone know how to fix the backbone during snugdock docking?

Many Thanks,

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Where is Sicdock application now? Can I find a substitute?

Category: 
Docking

Greetings,

       I am trying to reproduce the results of paper "Computational design of a homotrimeric metalloprotein with a trisbipyridyl core". I found that this research used an application named sicdock.ompstatic.linuxgccrelease to carry out docking calculations. But I can't find it in newly released Rosetta version. My foucs on Macbook can't find any application related to sicdock but only some options file and .cc file.

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Ligand Rotamer Control in Macther

Category: 
Docking

I am trying to run matcher with several residue constraints, and have already benchmarked the constraints individually and combined. Problem is that my ligand has several rotamers and once I enable the rotamers consideration in the matcher, the match enumeration makes the run impractical. I could solve this by removing the ligand rotamer consideration for the constraints that don't need it. Is there a way to do this for individual constraints?

 

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Save silent results to individual directory by process ID

Category: 
Docking

Hi all,

I'm running the docking_protocol application by mpirun, and I want to save silent results to individual directories determined by process ID. 

I found the option "-out:path:mpi_rank_dir" may be helpful but it didn't work. How do I use this option properly? 

 

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Prepacking a macrocycle for docking / preserving cyclization

Category: 
Docking

Dear all,

I have a macrocycle peptide obtained with simple_cycpep_predict, cycled between a Lys (Dap, Dab, and Orn too) side chain and the C-terminal carboxyl. I want to dock this peptide in a binding site with FlexPepDock. During the prepacking step, the bond between the Lys_NZ and the C atom that make the cyclization is lost and a carboxyl is restituted in the C-terminal.

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