exit code 1 - Si in ligand
log in

Advanced search

Message boards : Number crunching : exit code 1 - Si in ligand

Author Message
Profile robertmiles
Send message
Joined: 22 Apr 13
Posts: 62
Credit: 436,328
RAC: 214
Message 2426 - Posted: 12 Jun 2015, 2:32:54 UTC

I've recently had the following results several times:

<core_client_version>7.4.42</core_client_version>
<![CDATA[
<message>
Incorrect function.
(0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

Receptor name: PF14_0309_3

Ligand name: CHEMBL197837_0


Parse error on line 11 in file "ligand": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
20:53:02 (2192): called boinc_finish(1)

</stderr_txt>
]]>

The receptor names vary, but the ligand names don't.

Does this mean that you should cancel all workunits using that ligand?

Profile Ben
Project administrator
Project developer
Project tester
Project scientist
Send message
Joined: 17 Nov 14
Posts: 316
Credit: 1
RAC: 0
Message 2427 - Posted: 12 Jun 2015, 18:57:46 UTC - in response to Message 2426.

I'll not generate new WU with this ligand. But cancelling WU already in the database is tricky, but I'll try.

Profile Ben
Project administrator
Project developer
Project tester
Project scientist
Send message
Joined: 17 Nov 14
Posts: 316
Credit: 1
RAC: 0
Message 2433 - Posted: 15 Jun 2015, 9:09:56 UTC - in response to Message 2426.

No more WUs with this ligand.

Some user may still have some WU in their host. They will probably have a fail to report task.

Ananas
Send message
Joined: 8 Jun 13
Posts: 128
Credit: 1,947,833
RAC: 0
Message 2440 - Posted: 15 Jun 2015, 21:18:51 UTC - in response to Message 2433.
Last modified: 15 Jun 2015, 21:30:35 UTC

As this type of error always seems to be caused by a lowercase letter in a ligand atom ...

This should list all atoms with a lowercase letter :

grep "^HETATM.*[a-z]" CHEM*


Or do something like this :
mkdir suspicious mv `grep -l "^HETATM.*[a-z]" CHEM*` suspicious rmdir suspicious 2>/dev/null


The last line is optional, it removes empty "suspicious" subdirectories but leaves those untouched that contain invalid ligand files. This might be helpful if you have to issue the command in several directories with ligand files.

Profile Ben
Project administrator
Project developer
Project tester
Project scientist
Send message
Joined: 17 Nov 14
Posts: 316
Credit: 1
RAC: 0
Message 2441 - Posted: 16 Jun 2015, 9:03:35 UTC - in response to Message 2440.

The ligands are BLOBS in the database :)

Richard Haselgrove
Send message
Joined: 30 May 15
Posts: 25
Credit: 1,979,129
RAC: 1,584
Message 2451 - Posted: 18 Jun 2015, 10:16:35 UTC

On a related note, I'm getting a block of errors on host 105080 with

Ligand name: CHEMBL1643748_0

Parse error on line 16 in file "ligand": ATOM syntax incorrect: "B" is not a valid AutoDock type.

Message boards : Number crunching : exit code 1 - Si in ligand


Main page · Your account · Message boards


Copyright © 2017 Dr Anthony Chubb