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Docking

snugdock(sequence position requested was greater than the number of residues in the pose)

Category: 
Docking

Dear users, 

When I did snugdock, my native input structure and snug input structure share the same number of residues and residue indexes, but the error still shows up "sequence position requested was greater than the number of residues in the pose".
I attach both files and appreciate any suggestion. Thanks!

Post Situation: 

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:

Post Situation: 

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

 

Post Situation: 

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!

Post Situation: 

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:

Post Situation: 

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,

Post Situation: 

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.

Post Situation: 

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