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Message boards : Number crunching : Beware of the monster

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Ananas
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Message 2234 - Posted: 6 Apr 2015, 6:40:13 UTC

Ligand DB00638_0, file size 65353 has 265 torsions and more than 500 atoms.

If you receive that one, don't expect to be able to send it back in time.

Don't expect to be able to send it back at all, as within the runtime sure the max # of timeouts has been reached and the server has given it up.

This is very likely the case for other DB00638_* too

Ant Chubb
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Message 2245 - Posted: 8 Apr 2015, 10:56:23 UTC - in response to Message 2234.

Oh no! That should not be in there. We set a cut-off of 20 torsions. I'll try to remove this, but it may be too late for the WU queue. If you get this please cancel the job and we'll make sure it does not appear in any repeat WUs.

Sorry about that.

ciao,
Ant

Ananas
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Message 2248 - Posted: 8 Apr 2015, 15:09:53 UTC - in response to Message 2245.
Last modified: 8 Apr 2015, 15:21:00 UTC

... We set a cut-off of 20 torsions. ...

Well, that obviously hasn't worked.

Some from the DB00290_xx series have as many as ~45 torsions, DB00014_xx and DB00520_xx usually more than 32 and there are a lot more like those.

Currently working on some DB00290_68, after I found that adrianxw managed to finish some of those, I'll try that too (so far I had aborted them, assuming they will run weeks) ;-)

REMARK WARNING: 32 MAX_TORS EXCEEDED!!! REMARK 46 active torsions: ... HETATM 122 C LIG 1 6.981 -3.112 0.243 1.00 0.00 0.078 C ENDBRANCH 119 120 ... TORSDOF 46



p.s.: If you cannot remove DB00638_xx from the database, remove them from the download server - that will result in a few permanent download errors but not waste CPU time.


p.p.s.: Just out of curiosity ... the reason why for example several DB00290 exist, is that somehow a similar mechanism as the pseudoknot bindings in RNAs, that produce different possible 3D structures? I'm not a pro in those things, so if you could keep your answer simple ... ;-) I approached the pseudoknots only from a technical side, but not really knowing what they do.

Profile Ben
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Message 2249 - Posted: 8 Apr 2015, 15:21:41 UTC - in response to Message 2248.

Ligand DB00638 no longer in the database. All WU removed.

frankhagen
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Message 2250 - Posted: 8 Apr 2015, 15:24:30 UTC - in response to Message 2245.

Oh no! That should not be in there. We set a cut-off of 20 torsions.


obviously someone turned bright and fixed that... ;)

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Message 2251 - Posted: 8 Apr 2015, 15:37:27 UTC - in response to Message 2250.

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Message 2252 - Posted: 8 Apr 2015, 18:02:18 UTC - in response to Message 2251.

Well this is the first time I have run across something this hard to crunch!! vina_361594_83935_25p_3 11 hours and still going, I just installed the latest linux kernel and hesitate to reboot, since with the suspend problem, I don't want to start over from scratch. Oh and the other one at 8 hours is 20MB larger in working size!!

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