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Thread: [Error] ATOM syntax incorrect - not a valid AutoDock type

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adriverhoef
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[Error] ATOM syntax incorrect - not a valid AutoDock type

Saw three WUs erroring out in the Result Log:

Parse error on line 20 in file ".\ZINC000169743708.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

Parse error on line 10 in file "./ZINC000169837418.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

Parse error on line 20 in file "./ZINC000169743809.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

FAHV_1000300_3j3y-iy-P1_11075_1-- 	Error		1/3/17 06:34:32 	1/3/17 07:51:22
FAHV_1000300_3j3y-iy-P1_10665_1-- 	Error		1/3/17 06:34:32 	1/3/17 07:51:22
FAHV_1000317_3j3y-iy-P1_Rigid_11996_1--	Error		1/3/17 06:34:32 	1/3/17 07:51:22

All my wingmen are erroring out, too.
Thought somebody might want to know ...

[Jan 4, 2017 12:20:21 PM]

Scott L
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20 year badge for Uncovering Genome Mysteries

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100 year badge for Microbiome Immunity Project

20 year badge for Africa Rainfall Project

100 year badge for OpenPandemics - COVID-19


Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

in the mass number of results for FA@H, 20K+ in the last few days, i have only seen one error

Result Name: FAHV_ 1000368_ 3j3y-3S-P2_ 15248_ 3--

<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
Incorrect function.
(0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
INFO: result number = 3
INFO: No state to restore. Start from the beginning.
[18:53:29] Number of tasks = 4
[18:53:29] Running task 0,CPU time at start of task 0 was 0.000000
[18:53:29] ./ZINC000169811458.pdbqt size = 11 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-3S-P2.pdbqt size = 2193 0

Parse error on line 14 in file ".\ZINC000169811458.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

Edit: This machine is a win 10 64bit that runs 24/7 so no starting and stopping.

----------------------------------------

PowerEdge C6105 AMD Opteron 4332HE 3GHZ x8 64 GB
Threadripper 1950x 3.4ghz OC 3.875ghz

----------------------------------------
[Edit 2 times, last edit by Scott L at Jan 8, 2017 4:34:03 PM]

[Jan 8, 2017 4:29:41 PM]

adriverhoef
Master Cruncher
The Netherlands
Joined: Apr 3, 2009
Post Count: 2346
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Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

I would say it's not a shocking number of WUs. Here's another one:

Result Name: FAHV_ 1000487_ 3j3q-8O-P2_ Rigid_ 17015_ 1--
<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
INFO: result number = 1
INFO: No state to restore. Start from the beginning.
[22:21:17] Number of tasks = 5
[22:21:17] Running task 0,CPU time at start of task 0 was 0.000000
[22:21:17] ./ZINC000001532216.pdbqt size = 22 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-8O-P2_Rigid.pdbqt size = 2171 0
[22:22:30] Finished task #0 cpu time used 70.996315
[22:22:30] Running task 1,CPU time at start of task 1 was 70.996315
[22:22:30] ./ZINC000012358911.pdbqt size = 14 7 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-8O-P2_Rigid.pdbqt size = 2171 0
[22:23:25] Finished task #1 cpu time used 54.043736
[22:23:25] Running task 2,CPU time at start of task 2 was 125.040051
[22:23:25] ./ZINC000169876613.pdbqt size = 22 4 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-8O-P2_Rigid.pdbqt size = 2171 0

Parse error on line 9 in file "./ZINC000169876613.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

[Jan 8, 2017 10:42:18 PM]

adriverhoef
Master Cruncher
The Netherlands
Joined: Apr 3, 2009
Post Count: 2346
Status: Offline
Project Badges:


Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

(see also this message from seippel)

Caught another one, as did 9 of my wingmen:

Workunit Status

Project Name: FightAIDS@Home - Vina
Created: 01/12/2017 23:28:30
Name: FAHV_1000623_3j3y-_y-P2_Rigid_6234
Minimum Quorum: 2
Replication: 2

FAHV_1000623_3j3y-_y-P2_Rigid_6234_9-- Linux 3.13.0-101-generic 734 Error 1/15/17 05:43:05 1/15/17 06:22:09 0.31 18.0 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_8-- Linux 4.4.36-8-default 734 Server Aborted 1/15/17 05:27:53 1/15/17 08:14:23 0.00 8.7 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_7-- Linux 3.13.0-65-generic 734 Error 1/15/17 05:26:40 1/15/17 05:43:02 0.23 7.8 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_6-- Linux 4.8.0-34-generic 734 Error 1/15/17 02:41:55 1/15/17 05:26:33 0.24 6.3 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_5-- Linux 3.13.0-46-generic 734 Error 1/15/17 02:24:21 1/15/17 02:41:36 0.25 10.3 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_4-- Linux 4.8.15-300.fc25.x86_64 734 Error 1/15/17 01:45:38 1/15/17 05:27:41 0.19 13.6 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_3-- Linux 2.6.32-642.11.1.el6.x86_64 734 Error 1/15/17 01:45:28 1/15/17 02:24:06 0.15 5.2 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_2-- Microsoft x64 Edition 734 Error 1/14/17 22:22:05 1/15/17 01:45:20 0.37 15.1 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_1-- MS Windows 7 Ultimate x64 Edition 734 Error 1/14/17 10:48:07 1/14/17 22:22:03 0.27 6.4 / 0.0
FAHV_1000623_3j3y-_y-P2_Rigid_6234_0-- MS Windows Vista Ultimate x64 Edition 734 Error 1/13/17 15:44:45 1/14/17 10:47:54 0.35 3.9 / 0.0

Result Log

<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
INFO: result number = 4
INFO: No state to restore. Start from the beginning.
[06:12:01] Number of tasks = 11
[06:12:01] Running task 0,CPU time at start of task 0 was 0.000000
[06:12:01] ./ZINC000026895132.pdbqt size = 10 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:13:14] Finished task #0 cpu time used 59.161259
[06:13:14] Running task 1,CPU time at start of task 1 was 59.161259
[06:13:14] ./ZINC000006092209_3.pdbqt size = 24 4 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:16:07] Finished task #1 cpu time used 141.830191
[06:16:07] Running task 2,CPU time at start of task 2 was 200.991450
[06:16:07] ./ZINC000000037833.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:17:59] Finished task #2 cpu time used 90.186458
[06:17:59] Running task 3,CPU time at start of task 3 was 291.177908
[06:17:59] ./ZINC000002163639.pdbqt size = 17 8 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:21:14] Finished task #3 cpu time used 157.748241
[06:21:14] Running task 4,CPU time at start of task 4 was 448.926149
[06:21:14] ./ZINC000005133565.pdbqt size = 14 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:23:03] Finished task #4 cpu time used 91.576435
[06:23:03] Running task 5,CPU time at start of task 5 was 540.502584
[06:23:03] ./ZINC000006070386_1.pdbqt size = 22 5 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0
[06:25:52] Finished task #5 cpu time used 138.262109
[06:25:52] Running task 6,CPU time at start of task 6 was 678.764693
[06:25:52] ./ZINC000169811458.pdbqt size = 11 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_y-P2_Rigid.pdbqt size = 2171 0

Parse error on line 14 in file "./ZINC000169811458.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

[Jan 15, 2017 11:10:48 AM]

Scott L
Senior Cruncher
United States
Joined: Jun 24, 2013
Post Count: 183
Status: Offline
Project Badges:


Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

checked my error results and found 2 more.

Result Name: FAHV_ 1000555_ 3j3y-_ M-P2_ Rigid_ 5407_ 0--

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<message>
Incorrect function.
(0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
INFO: result number = 0
INFO: No state to restore. Start from the beginning.
[21:30:56] Number of tasks = 11
[21:30:56] Running task 0,CPU time at start of task 0 was 0.000000
[21:30:56] ./ZINC000169837418.pdbqt size = 18 6 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-_M-P2_Rigid.pdbqt size = 2171 0

Parse error on line 10 in file ".\ZINC000169837418.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

Result Name: FAHV_ 1000589_ 3j3q-_ w-P2_ Rigid_ 7218_ 1--

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<message>
Incorrect function.
(0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
INFO: result number = 1
INFO: No state to restore. Start from the beginning.
[10:16:12] Number of tasks = 9
[10:16:12] Running task 0,CPU time at start of task 0 was 0.000000
[10:16:12] ./ZINC000005133565.pdbqt size = 14 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_w-P2_Rigid.pdbqt size = 2171 0
[10:19:15] Finished task #0 cpu time used 183.004773
[10:19:15] Running task 1,CPU time at start of task 1 was 183.004773
[10:19:15] ./ZINC000006070386_1.pdbqt size = 22 5 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_w-P2_Rigid.pdbqt size = 2171 0
[10:23:44] Finished task #1 cpu time used 268.134519
[10:23:44] Running task 2,CPU time at start of task 2 was 451.139292
[10:23:44] ./ZINC000169811458.pdbqt size = 11 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_w-P2_Rigid.pdbqt size = 2171 0

Parse error on line 14 in file ".\ZINC000169811458.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

----------------------------------------

PowerEdge C6105 AMD Opteron 4332HE 3GHZ x8 64 GB
Threadripper 1950x 3.4ghz OC 3.875ghz

[Jan 15, 2017 2:19:16 PM]

adriverhoef
Master Cruncher
The Netherlands
Joined: Apr 3, 2009
Post Count: 2346
Status: Offline
Project Badges:


Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

(see also this message from seippel)

Caught ~~two more~~ another three:
1.
Workunit Status
Project Name: FightAIDS@Home - Vina
Created: 01/19/2017 12:30:00
Name: FAHV_1000725_3j3q-_9-P3_Rigid_4987
Minimum Quorum: 2
Replication: 2

FAHV_1000725_3j3q-_9-P3_Rigid_4987_9-- Linux     734  Error           1/21/17 07:58:34  1/21/17 08:29:40  0.47    16.4/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_8-- Linux     734  Server Aborted  1/21/17 06:51:17  1/21/17 08:36:41  0.00     0.0/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_7-- Linux     734  Error           1/21/17 05:19:23  1/21/17 07:58:28  0.34    25.7/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_6-- Linux     734  Error           1/20/17 19:57:25  1/21/17 06:51:14  0.32    19.6/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_5-- Linux     734  Error           1/20/17 17:48:30  1/21/17 05:19:14  0.37    22.2/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_4-- Linux     734  Error           1/20/17 17:17:22  1/20/17 17:48:12  0.47    11.3/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_3-- Linux     734  Error           1/20/17 17:17:19  1/20/17 19:57:21  0.27    13.0/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_2-- Linux     734  Error           1/20/17 15:14:17  1/20/17 17:17:18  0.40     9.1/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_1-- MSWin 10  734  Error           1/20/17 06:54:52  1/20/17 15:14:12  0.57    16.3/0.0
FAHV_1000725_3j3q-_9-P3_Rigid_4987_0-- Android   734  Error           1/19/17 12:30:05  1/20/17 06:54:37  1.77    19.4/0.0

Result Log
Result Name: FAHV_ 1000725_ 3j3q-_ 9-P3_ Rigid_ 4987_ 7--
<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
INFO: result number = 7
INFO: No state to restore. Start from the beginning.
[08:32:19] Number of tasks = 12
[08:32:19] Running task 0,CPU time at start of task 0 was 0.000000
[08:32:19] ./ZINC000004347351.pdbqt size = 24 4 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:35:04] Finished task #0 cpu time used 134.709482
[08:35:04] Running task 1,CPU time at start of task 1 was 134.709482
[08:35:04] ./ZINC000002510205.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:37:37] Finished task #1 cpu time used 130.502993
[08:37:37] Running task 2,CPU time at start of task 2 was 265.212475
[08:37:37] ./ZINC000000113784.pdbqt size = 17 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:38:53] Finished task #2 cpu time used 64.027923
[08:38:53] Running task 3,CPU time at start of task 3 was 329.240398
[08:38:53] ./ZINC000001047416.pdbqt size = 23 7 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:42:11] Finished task #3 cpu time used 165.729171
[08:42:11] Running task 4,CPU time at start of task 4 was 494.969569
[08:42:11] ./ZINC000000111684.pdbqt size = 15 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:43:41] Finished task #4 cpu time used 72.212382
[08:43:41] Running task 5,CPU time at start of task 5 was 567.181951
[08:43:41] ./ZINC000004390627.pdbqt size = 20 5 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:46:03] Finished task #5 cpu time used 117.102203
[08:46:03] Running task 6,CPU time at start of task 6 was 684.284154
[08:46:03] ./ZINC000000159043.pdbqt size = 13 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:47:02] Finished task #6 cpu time used 50.904505
[08:47:02] Running task 7,CPU time at start of task 7 was 735.188659
[08:47:02] ./ZINC000001039627.pdbqt size = 26 6 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:50:33] Finished task #7 cpu time used 177.044899
[08:50:33] Running task 8,CPU time at start of task 8 was 912.233558
[08:50:33] ./ZINC000000124070.pdbqt size = 24 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:52:46] Finished task #8 cpu time used 108.260504
[08:52:46] Running task 9,CPU time at start of task 9 was 1020.494062
[08:52:46] ./ZINC000001047898.pdbqt size = 30 7 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0
[08:57:04] Finished task #9 cpu time used 216.047655
[08:57:04] Running task 10,CPU time at start of task 10 was 1236.541717
[08:57:04] ./ZINC000169743708.pdbqt size = 20 4 ../../projects/www.worldcommunitygrid.org/fahv.3j3q-_9-P3_Rigid.pdbqt size = 4370 0

Parse error on line 20 in file "./ZINC000169743708.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

2. (EDIT: and got credited individually, too)
Workunit Status
Project Name: FightAIDS@Home - Vina
Created: 01/17/2017 12:29:41
Name: FAHV_1000640_4xfx_P3_4703
Minimum Quorum: 1
Replication: 1

FAHV_1000640_4xfx_P3_4703_8-- Linux     734  Error  1/21/17 05:02:14  1/21/17 19:27:43  0.04     1.1/1.1
FAHV_1000640_4xfx_P3_4703_7-- MS        734  Error  1/21/17 04:56:47  1/21/17 05:02:07  0.04     2.0/2.0
FAHV_1000640_4xfx_P3_4703_6-- Linux     734  Error  1/20/17 22:57:48  1/21/17 04:56:40  0.02     0.8/0.8
FAHV_1000640_4xfx_P3_4703_5-- MSWin 10  734  Error  1/20/17 21:38:18  1/20/17 22:57:42  0.02     0.8/0.8
FAHV_1000640_4xfx_P3_4703_4-- MSWin 7   734  Error  1/19/17 03:41:16  1/20/17 21:38:13  0.03     2.2/2.2
FAHV_1000640_4xfx_P3_4703_3-- Darwin    734  Error  1/18/17 20:40:59  1/19/17 03:41:14  0.01     1.0/0.0
FAHV_1000640_4xfx_P3_4703_2-- MSWin 10  734  Error  1/18/17 20:35:35  1/18/17 20:40:57  0.03     1.0/1.0
FAHV_1000640_4xfx_P3_4703_1-- MSWin 7   734  Error  1/18/17 17:57:13  1/18/17 20:35:34  0.03     0.8/0.8
FAHV_1000640_4xfx_P3_4703_0-- MSWin 7   734  Error  1/17/17 12:29:49  1/18/17 17:57:07  0.06     0.6/0.6

Result Log
Result Name: FAHV_ 1000640_ 4xfx_ P3_ 4703_ 6--
<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
INFO: result number = 6
INFO: No state to restore. Start from the beginning.
[05:53:56] Number of tasks = 16
[05:53:56] Running task 0,CPU time at start of task 0 was 0.000000
[05:53:56] ./ZINC000012370779.pdbqt size = 21 5 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0
[05:54:17] Finished task #0 cpu time used 19.513978
[05:54:17] Running task 1,CPU time at start of task 1 was 19.513978
[05:54:17] ./ZINC000000039684.pdbqt size = 10 2 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0
[05:54:22] Finished task #1 cpu time used 4.913270
[05:54:22] Running task 2,CPU time at start of task 2 was 24.427248
[05:54:22] ./ZINC000000165412.pdbqt size = 20 6 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0
[05:54:45] Finished task #2 cpu time used 22.766185
[05:54:45] Running task 3,CPU time at start of task 3 was 47.193433
[05:54:45] ./ZINC000000111810.pdbqt size = 14 3 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0
[05:54:54] Finished task #3 cpu time used 7.901143
[05:54:54] Running task 4,CPU time at start of task 4 was 55.094576
[05:54:54] ./ZINC000016124447.pdbqt size = 12 3 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0
[05:55:01] Finished task #4 cpu time used 6.798925
[05:55:01] Running task 5,CPU time at start of task 5 was 61.893501
[05:55:01] ./ZINC000169743141.pdbqt size = 9 1 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P3.pdbqt size = 4082 0

Parse error on line 12 in file "./ZINC000169743141.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

3.
Workunit Status
Project Name: FightAIDS@Home - Vina
Created: 01/21/2017 12:33:26
Name: FAHV_1000793_3j3y-gO-P3_Rigid_5994
Minimum Quorum: 1
Replication: 1

FAHV_1000793_3j3y-gO-P3_Rigid_5994_8-- MSWin 10   734  Error  1/23/17 11:23:42  1/23/17 11:42:33  0.20     9.2/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_7-- MSWin 10   734  Error  1/23/17 08:25:05  1/23/17 11:23:31  0.18     6.6/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_6-- MSWin 8.1  734  Error  1/22/17 23:25:54  1/23/17 08:24:48  0.18    13.5/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_5-- Linux      734  Error  1/22/17 06:47:23  1/22/17 23:25:47  0.07     8.5/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_4-- Linux      734  Error  1/22/17 02:41:10  1/22/17 06:47:04  0.06     3.3/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_3-- MSWin 7    734  Error  1/21/17 23:25:24  1/22/17 02:41:05  0.14     4.6/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_2-- MSWin 7    734  Error  1/21/17 18:39:15  1/21/17 23:25:14  0.14     4.4/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_1-- MSWin 7    734  Error  1/21/17 16:05:53  1/21/17 18:39:11  0.22     3.9/0.0
FAHV_1000793_3j3y-gO-P3_Rigid_5994_0-- Linux      734  Error  1/21/17 12:33:34  1/21/17 16:05:46  0.09     8.6/0.0

Result Log
Result Name: FAHV_ 1000793_ 3j3y-gO-P3_ Rigid_ 5994_ 0--
<core_client_version>7.6.22</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt>
INFO: result number = 0
INFO: No state to restore. Start from the beginning.
[16:58:22] Number of tasks = 10
[16:58:22] Running task 0,CPU time at start of task 0 was 0.000000
[16:58:22] ./ZINC000002163639.pdbqt size = 17 8 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-gO-P3_Rigid.pdbqt size = 4365 0
[17:00:33] Finished task #0 cpu time used 122.045300
[17:00:33] Running task 1,CPU time at start of task 1 was 122.045300
[17:00:33] ./ZINC000005133565.pdbqt size = 14 3 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-gO-P3_Rigid.pdbqt size = 4365 0
[17:01:50] Finished task #1 cpu time used 72.926331
[17:01:50] Running task 2,CPU time at start of task 2 was 194.971631
[17:01:50] ./ZINC000006070386_1.pdbqt size = 22 5 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-gO-P3_Rigid.pdbqt size = 4365 0
[17:03:49] Finished task #2 cpu time used 113.149138
[17:03:49] Running task 3,CPU time at start of task 3 was 308.120769
[17:03:49] ./ZINC000169811458.pdbqt size = 11 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-gO-P3_Rigid.pdbqt size = 4365 0

Parse error on line 14 in file "./ZINC000169811458.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive.
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

----------------------------------------
[Edit 4 times, last edit by adriverhoef at Jan 23, 2017 3:21:58 PM]

[Jan 21, 2017 11:53:51 AM]

seippel
Former World Community Grid Tech
Joined: Apr 16, 2009
Post Count: 392
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Re: [Error] ATOM syntax incorrect - not a valid AutoDock type

The ligand files that were causing the "ATOM syntax incorrect: "Si" is not a valid AutoDock type" error have been filter from batch inputs and the ones that have errored out completely have been fixed and are currently being re-run (some have already completed successfully). There may be a few resends of the bad ones lingering out there, but these should be effectively eliminated going forward.

Seippel

[Jan 26, 2017 11:53:05 PM]

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