Parse error on line 6 in file "vina_data.pdbqt":

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Profile Dingo
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Message 4681 - Posted: 30 Jan 2017, 23:33:39 UTC
Last modified: 30 Jan 2017, 23:35:08 UTC

This error started appearing again today on Linux machines

This is from https://boinc.drugdiscoveryathome.com/show_host_detail.php?hostid=1405

<core_client_version>7.4.23</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
17:40:20 (16762): wrapper (7.5.26014): starting
17:40:20 (16762): wrapper: running vina (--cpu 1 --config conf.txt --ligand vina_data.pdbqt --out vina_out.pdbqt --log vina_log.txt)


Parse error on line 6 in file "vina_data.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
17:40:21 (16762): vina exited; CPU time 0.032000
17:40:21 (16762): app exit status: 0x100
17:40:21 (16762): called boinc_finish(195)

</stderr_txt>

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Message 4682 - Posted: 31 Jan 2017, 0:09:23 UTC
Last modified: 31 Jan 2017, 0:21:51 UTC

Hey Dingo, like you i've been getting this error too. I'm getting hundreds of these but on windows with vina.

on just one PC i've had 120+ computation errors in the last 24hrs. Most if not all with the same or similar error.

195 (0x000000C3) EXIT_CHILD_FAILED.

Looking In task details most have an invalid data type like below, so it looks like it's the same error on both window & linux...

Parse error on line 44 in file "vina_data.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
01:52:16 (2000): vina.exe exited; CPU time 0.000000

While most end within the first sec or two those seconds add up. The FIND project had the same problems with vina.
Anything that could be done to reduce the numbers would be good.

Examples:
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6372201
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6372236
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6372237
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6365941
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6365940
https://boinc.drugdiscoveryathome.com/workunit.php?wuid=6372201

There are hundreds more examples if you need them.

If this is considered normal behaviour for vina with this data set please let us know?
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Message 4686 - Posted: 31 Jan 2017, 7:18:27 UTC

SAME HERE. Have had several tasks with same error over last 24+ hours.

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Message boards : Number crunching : Parse error on line 6 in file "vina_data.pdbqt":


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