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Martin Schnellinger
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Trying to understand the open pandemics workunit log together

Trying to understand the open pandemics workunit log together

Result Name: OPN1_ 0013734_ 05717_ 0--
<core_client_version>7.2.47</core_client_version>
<![CDATA[
<stderr_txt>
INFO:[12:28:33] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[12:29:16] End AutoGrid...
INFO:[12:29:17] Start AutoDock for ZINC000775778779-ACR3.34_RX1--4mm3_001_tyr264-HO--CYS112_wcgsplit2.dpf(Job #0)...
INFO: In AutoDock main_autodock()
Beginning AutoDock...
INFO: Setting num_generations: 27000
About to enter main loop...(dockings already completed: 0)
INFO:[12:35:53] Finished Docking number 0
INFO:[12:41:42] Finished Docking number 1
INFO:[12:48:40] Finished Docking number 2
INFO:[12:54:28] Finished Docking number 3
INFO:[13:00:24] Finished Docking number 4
INFO:[13:06:19] Finished Docking number 5
INFO:[13:12:11] Finished Docking number 6
INFO:[13:18:13] Finished Docking number 7
INFO:[13:23:51] Finished Docking number 8
INFO:[13:29:53] Finished Docking number 9
INFO:[13:35:57] Finished Docking number 10
INFO:[13:41:38] Finished Docking number 11
INFO:[13:47:41] Finished Docking number 12
INFO:[13:53:35] Finished Docking number 13
INFO:[13:59:30] Finished Docking number 14
INFO:[14:05:23] Finished Docking number 15
INFO:[14:11:48] Finished Docking number 16
INFO:[14:17:55] Finished Docking number 17
INFO:[14:23:43] Finished Docking number 18
INFO:[14:30:49] Finished Docking number 19
INFO:[14:37:45] Finished Docking number 20
INFO:[14:42:55] Finished Docking number 21
INFO:[14:48:08] Finished Docking number 22
INFO:[14:53:58] Finished Docking number 23
INFO:[14:59:29] Finished Docking number 24
INFO:[15:04:45] Finished Docking number 25
INFO:[15:10:25] Finished Docking number 26
INFO:[15:15:40] Finished Docking number 27
INFO:[15:20:54] Finished Docking number 28
INFO:[15:20:55] End AutoDock...
INFO:Cpu time = 9417.234366
15:20:55 (2520): called boinc_finish(0)

</stderr_txt>
]]>

Dear fellow crunchers,
to me, it seems useful to undestand open pandemics work unit log.
Above, there is one log text.
Let's discuss it.

The clue of understanding the log probably means having to understand, what ZINC000775778779-ACR3.34_RX1--4mm3_001_tyr264-HO--CYS112_wcgsplit2.dpf means.

The data file ending "dpf" means that the file is in the format of IBM's Db2 data management products (https://en.wikipedia.org/wiki/IBM_Db2_Family)

Is ZINC the name of the chemical substance being investigated? Does that mean the the machine is checking whether the substance ZINC can be docked to the Viruses surface?

Let`s try to undestand the log together. Comments very welcome.

Greetings and all the best.
M
[Oct 14, 2020 7:07:42 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Aurum
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Re: Trying to understand the open pandemics workunit log together

ZINC is a database of molecules: https://zinc.docking.org/

Well, that's the extent of my knowledge on this topic.
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[Oct 14, 2020 7:35:20 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Falconet
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Re: Trying to understand the open pandemics workunit log together

As Aurum said, ZINC is the name of a public database that hosts lots of molecules, compounds, substances, whatever.

The number that comes after ZINC is reference to whatever substance is being docked against a SARS-CoV-2 protein target - In the case of that workunit, this is the substance http://zinc.docking.org/substances/ZINC000775778779/

As for the rest, I have no idea. Could be the specific region/pocket/whatever of the target protein, of which the substance is being docked against.
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[Oct 14, 2020 7:51:02 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Martin Schnellinger
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rose Re: Trying to understand the open pandemics workunit log together

Hello,
thank you very much. Friendly, fast, good information.
I hope that this thread will be useful for everyone, no matter whether cruncher, guest or scientist.

Maybe there is someone out there who knows the rest i.e. -ACR3.34_RX1--4mm3_001_tyr264-HO--CYS112_wcgsplit2?

Thanks again and all the best.
Martin
[Oct 14, 2020 8:28:54 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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