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Docking

"in_progress" decoy files in some docking2 local_docking job tar archives

Category: 
Docking

In one of my ROSIE docking2 local_docking jobs (17702), I noticed that its tar archive's output\trigger-00001.dock folder contained several files like proteins_0130.in_progress.bz2 with the unusual size of 42 bytes in addition to many files like proteins_0129.pdb.bz2 and proteins_0131.pdb.bz2 with the more typical size of 82-84 kbytes. Do you know what causes these "in_progress" files to occur and how I can prevent them from occurring? Is the cure as simple as re-opening the job's web page and then reloading its tar archive file?

Thanks!

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Fnat=NaN in a docking2 job

Category: 
Docking

One of my docking2 docking_local_refine jobs (#17790) output many structures with Fnat=NaN. I am used to seeing Fnat near 1 when the rms value is low and Fnat near 0 when the rms value is high. What would make Fnat give a value of NaN? Should I trust the other scores given for this run? How can I prevent future runs from giving Fnat=NaN?

Thanks!

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Running time of Rosetta/FlexPepDock

Category: 
Docking

Hello everyone, and thanks for reading this!

My question is about the running time of a docking. I need to dock several same length peptides to a small protein. I have a around 55 nodes for this job. My question is should i put 1 job for each node, or should i do the jobs one by one and assig each job to the 55 cores with MPI?

Thanks!

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Ways to improve ROSIE docking2 jobs

Category: 
Docking

(1) By the images of various output pdb files, be more clear that these are ones with the ten lowest I_sc (interface energy) scores.

(2) In the instructions, give more details about the differences between local_docking and docking_local_refine protocols.

(3) For each docking_local_refine job, please let every output pdb file listed in score.sf have a unique name and include all these pdb files in the tar archive file for the job.

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Ways to improve both docking2 and symmetric_docking jobs

Category: 
Docking

(1) When you click on a point in a plot, a window appears listing data for that point. Often the cursor blocks the top line of this window. Could you add a blank line to the top of this window so the cursor doesn't block any important data?

(2) Could you prevent job names from ending with blanks, /, or \ characters? I have tried automatically fishing results out of the resultant tar files using Matlab, but Matlab has given trouble when the job names end with blanks. I'd imagine job names with / or \ in them could cause similar problems.

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Use NMR ensemble in protein-protein docking?

Category: 
Docking

I want to dock two proteins, A and B. I have pdb files for both of them, A.pdb and B.pdb. Now, A.pdb is an X-ray structure, while B.pdb is an NMR ensemble. Is it possible to run a docking simulation with these inputs? How can I do it?

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Fnat and Irms are nan in score.sc from docking_protocol?

Category: 
Docking

I am running a docking_protocol for two proteins. Inspecting the score.sc file, I find that the columns Fnat and Irms are "nan" (Not A Number, I suppose). Why could this be happening? I can post more details if needed.

(BTW, what does Fnat mean?)

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Antibody Docking application

Category: 
Docking

Hi, 

I want to do docking antibody-antigen complex. Understanding from literature, ensemble docking and snug dock is better for Ab-ag. But I didn’t find a complete tutorial or documentation for snug dock. I found just the page in the following link that is some confusing:

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock

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