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World Community Grid Forums
Category: Active Research
Forum: OpenPandemics - COVID-19 Project
Thread: New OPNG targets. Strange Warnings in the stderr file |
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Thread Status: Active Total posts in this thread: 6
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Grumpy Swede
Master Cruncher Svíþjóð Joined: Apr 10, 2020 Post Count: 2106 Status: Offline Project Badges: 
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I have noticed some warnings in the results stderr files in the new targets. So far I have only crunched a few tasks, but the warning is in all of them. I'm sure the OPN scientists can explain this, and that it doesn't matter for the science.
----------------------------------------autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4325 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4326 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4331 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4332 example task: https://www.worldcommunitygrid.org/contribution/workunit/294252123 Edit, added: And so far the OPNG validator doesn't want to even visit these "new" OPNG tasks. Another Edit: The validator woke up, and validated my "new" OPNG tasks. The warning messages obviously didn't matter. [Edit 7 times, last edit by Grumpy Swede at Apr 28, 2023 4:02:43 PM] |
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TPCBF
Master Cruncher USA Joined: Jan 2, 2011 Post Count: 1934 Status: Recently Active Project Badges: 
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I have noticed some warnings in the results stderr files in the new targets. So far I have only crunched a few tasks, but the warning is in all of them. I'm sure the OPN scientists can explain this, and that it doesn't matter for the science. I don't know about the validator running or not (haven't checked my results page yet), but I noticed that the earlier batches of OPNG WUs, that ran for only 4-6min, have now been replaced/succeeded by batches that run again in the 25-35min range.autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4325 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4326 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4331 autogrid4: WARNING: Found an H-bonding atom with three bonded atoms, atom serial number 4332 example task: https://www.worldcommunitygrid.org/contribution/workunit/294252123 Edit, added: And so far the OPNG validator doesn't want to even visit these "new" OPNG tasks. Another Edit: The validator woke up, and validated my "new" OPNG tasks. The warning messages obviously didn't matter. Would be nice if WCG, instead of continuing playing child's games, would provide some more timely info about what is being send out...  Ralf  |
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alanb1951
Veteran Cruncher Joined: Jan 20, 2006 Post Count: 884 Status: Offline Project Badges: 
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For information (and a possible explanation):
----------------------------------------There currently seem to be 5rl7_nuc_0--ASER289 [5387 atoms] (As far as I am aware, the grid dimension (npts) and centre do not change for a given target name.) As far as I can tell from the tasks I've returned so far, 5rl7_nuc_0--ASER289 doesn't appear to show any of those warnings, but all the others do. Looking at the atoms around the warning points shows that those four receptors all have the same sequence at that point (subject to slight differences in co-ordinates!) The residue code is MET (Methionine?) with sequence number 474, and the character before the code is A or B -- this is apparently an "alternate location indicator." The receptor that doesn't produce warnings has a MET 474 sequence as well, but it doesn't have any alternate location indicators, so no A/B pairing and only 9 atoms! I don't know what should happen with those alternate locations, but it seems to be what has prompted the warnings :-) Cheers - Al. [Edited to remove a reference to a message by Aurum that only showed up underneath the edit pane whilst I was compiling this, and is not visible in the main thread, removing context from what I'd written based on it! Also fixed a typo. Edited again to add another receptor and a possible explanation for the warnings... Some rewording!]] [Edit 4 times, last edit by alanb1951 at Apr 29, 2023 2:37:10 AM] |
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alanb1951
Veteran Cruncher Joined: Jan 20, 2006 Post Count: 884 Status: Offline Project Badges:
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For information...
Three more receptors have appeared, and two of them show the same sort of warnings as mentioned above (and for the same sequence (MET 474) 7nng_nuc_0--ASER289 has no warnings; 5rmm_rna5_0--BASN179 and 5rmc_rna31_0--BSER236 have warnings. These receptors are about the same size as the earlier ones in this set, and use similar grid sizes. Cheers - Al. |
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