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Prepacking crashing using metalloprotein
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
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
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
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
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?
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.
Ligand Rotamer Control in Macther
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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Small molecule dimer/trimer/etc docking
Hello,
Is it possible to coax rosetta to dock, say, a predefined dimer or trimer of small molecules to presumed binding site ona protein ? Rigid body ligand is OK.
thanks,
lukasz
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Save silent results to individual directory by process ID
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?