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adriverhoef
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The Netherlands
Joined: Apr 3, 2009
Post Count: 2104
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[Error] No atoms in the ligand

Saw this error popping up, just like in post 547966 (from 2017) and post 608154 (from 2019):
workunit 380115144
SCC1_0004356_KLF15-A_38697_0  MSWin 10      Error  2023-09-18T04:31:52  2023-09-19T21:27:34    0.00/0.00
SCC1_0004356_KLF15-A_38697_1 Linux Ubuntu Error 2023-09-19T21:27:41 2023-09-20T02:02:40 0.00/0.00
SCC1_0004356_KLF15-A_38697_2 Wait. 0.00/0.00
Details: ---------------------------------------------------------------------------------------------------------------------------------------
SCC1_0004356_KLF15-A_38697_0  MSWin 10      Error  2023-09-18T04:31:52  2023-09-19T21:27:34    0.00/0.00
Logfile:
<core_client_version>7.16.11</core_client_version>
<message>
Incorrect function.
(0x1) - exit code 1 (0x1)</message>
<stderr_txt>
INFO: result number = 0
INFO: No state to restore. Start from the beginning.
[16:45:47] Number of tasks = 1
[16:45:47] Running task 0,CPU time at start of task 0 was 0.000000
[16:45:47] ./cmpd-4738697.pdbqt size = 0 0 ../../projects/www.worldcommunitygrid.org/scc1.KLF15-A.pdbqt size = 403 0


Parse error on line 0 in file ".\cmpd-4738697.pdbqt": No atoms in the ligand
VINA failed. rc = 1. Exiting

</stderr_txt>
SCC1_0004356_KLF15-A_38697_1 Linux Ubuntu Error 2023-09-19T21:27:41 2023-09-20T02:02:40 0.00/0.00
Logfile:
<core_client_version>7.16.6</core_client_version>
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
INFO: result number = 1
INFO: No state to restore. Start from the beginning.
[04:01:41] Number of tasks = 1
[04:01:41] Running task 0,CPU time at start of task 0 was 0.000000
[04:01:41] ./cmpd-4738697.pdbqt size = 0 0 ../../projects/www.worldcommunitygrid.org/scc1.KLF15-A.pdbqt size = 403 0


Parse error on line 0 in file "./cmpd-4738697.pdbqt": No atoms in the ligand
VINA failed. rc = 1. Exiting

</stderr_txt>
SCC1_0004356_KLF15-A_38697_2 Waiting to be sent 0.00/0.00


Out of 10,000 completed SCC1-tasks available in my Results, this was the only one with the error.
Inspection of 20 surrounding workunits (380115134 to 380115154) also didn't reveal any errors.

According to Seippel in post 417882:
The pdbqt line in the output give information about two pdbqt files being docked. The first is the ligand being docked and the second is the receptor site (which is why it's larger). The two numbers after each give information about the number of atoms and branches for each.

Adri
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[Edit 1 times, last edit by adriverhoef at Sep 20, 2023 9:27:13 AM]
[Sep 20, 2023 9:23:09 AM]   Link   Report threatening or abusive post: please login first  Go to top 
TigerLily
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Re: [Error] No atoms in the ligand

Hi Adri,

Thanks for sharing this. I forwarded this to the tech team.
[Sep 20, 2023 5:21:44 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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