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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?
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?
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?
(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.
(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.
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?
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?)