"Si" is not a valid AutoDock type.

Message boards : Number crunching : "Si" is not a valid AutoDock type.

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Dirk Broer

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Message 4691 - Posted: 1 Feb 2017, 10:13:45 UTC

Parse error on line 14 in file "vina_data.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.

This error message is reported on both my Windows and my Linux boxes. When I check the work unit other crunchers have had the same errror for that WU.
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4696 - Posted: 2 Feb 2017, 16:49:17 UTC - in response to Message 4691.  

It's an expected error when one uses database like pubchem. Unfortunately our docking programms work only on limited chemical space and structures with Si don't belong to it. Fortunately they are rarely compounds of interest. So I think if it is not a common error we can safely ignore it
Krzysztof 'krzyszp' Piszczek

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Aurimas

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Message 4697 - Posted: 2 Feb 2017, 17:39:59 UTC - in response to Message 4696.  

It's an expected error when one uses database like pubchem. Unfortunately our docking programms work only on limited chemical space and structures with Si don't belong to it. Fortunately they are rarely compounds of interest. So I think if it is not a common error we can safely ignore it


Unfortunately I have 102 tasks with this error in last few days. So these errors are not very rare...
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JugNut

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Message 4699 - Posted: 3 Feb 2017, 1:18:48 UTC - in response to Message 4697.  
Last modified: 3 Feb 2017, 1:29:37 UTC

It's an expected error when one uses database like pubchem. Unfortunately our docking programms work only on limited chemical space and structures with Si don't belong to it. Fortunately they are rarely compounds of interest. So I think if it is not a common error we can safely ignore it


Unfortunately I have 102 tasks with this error in last few days. So these errors are not very rare...



I'm with you Aurimas I have the same amount on just one PC,
https://boinc.drugdiscoveryathome.com/results.php?hostid=1900&offset=0&show_names=0&state=6&appid=

This was also mentioned in this other thread. https://boinc.drugdiscoveryathome.com/forum_thread.php?id=2067
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Crystal Pellet

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Message 4705 - Posted: 4 Feb 2017, 14:58:32 UTC

I got 149 of those errors within 8 hours, so not really rare. Loss of run time is no problem - only 2 seconds each -

but after an error deferring communication from client to server is increased from minutes up to 24 hours and avoids getting new tasks.
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Yavanius
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Message 4722 - Posted: 7 Feb 2017, 5:24:14 UTC

I'm getting them now too. 4 WUs in a row.
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Yavanius
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Message 4723 - Posted: 7 Feb 2017, 5:30:54 UTC

Why do they have Si in them if you can't process them??
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Message boards : Number crunching : "Si" is not a valid AutoDock type.


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