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Thread Status: Active Total posts in this thread: 4
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Martin Schnellinger
Advanced Cruncher Joined: Apr 29, 2007 Post Count: 128 Status: Offline Project Badges:
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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 |
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Aurum
Master Cruncher The Great Basin Joined: Dec 24, 2017 Post Count: 2391 Status: Offline Project Badges:
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ZINC is a database of molecules: https://zinc.docking.org/
----------------------------------------Well, that's the extent of my knowledge on this topic. ![]() ...KRI please cancel all shadow-banning |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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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. ![]() - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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Martin Schnellinger
Advanced Cruncher Joined: Apr 29, 2007 Post Count: 128 Status: Offline Project Badges:
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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 |
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