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  Thread: [Error] ATOM syntax incorrect: "62 " is not a valid atom number

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adriverhoef
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[Error] ATOM syntax incorrect: "62 " is not a valid atom number
Just found this error in a workunit:
workunit 298010340
SCC1_0004175_MyoD1-C_0002_0  Linux Ubuntu  Error  2023-05-15T20:16:14  2023-05-15T20:43:06    0.00/0.00
SCC1_0004175_MyoD1-C_0002_1  Fedora Linux  Error  2023-05-15T20:43:09  2023-05-15T20:45:16    0.00/0.00
SCC1_0004175_MyoD1-C_0002_2  MSWin 10      InPrg  2023-05-15T20:45:18  2023-05-18T20:45:18    0.00/0.00
---------------------------------------------------------------------------------------------------------------------------------------
Details:
SCC1_0004175_MyoD1-C_0002_0  Linux Ubuntu  Error  2023-05-15T20:16:14  2023-05-15T20:43:06    0.00/0.00
	Logfile:
	<core_client_version>7.16.11</core_client_version>
	<message>
	process exited with code 1 (0x1, -255)</message>
	<stderr_txt>
	INFO: result number = 0
	INFO: No state to restore.  Start from the beginning.
	[22:42:05] Number of tasks = 1
	[22:42:05] Running task 0,CPU time at start of task 0 was 0.000000
	[22:42:05] ./cmpd-1000002.pdbqt size = 26 3 ../../projects/www.worldcommunitygrid.org/scc1.MyoD1-C.pdbqt size = 1268 0
	
	
	Parse error on line 190 in file "../../projects/www.worldcommunitygrid.org/54b50c489807ec5f5c73bed087c7ea12.pdbqt": ATOM syntax incorrect: "62 " is not a valid atom number
	VINA failed.  rc = 1.  Exiting
	
	</stderr_txt>

The task starts and apparently crashes immediately, as the runtime (CpuTime) is shown as exactly 0.0 in the API:
App	Claimed	CpuTime	Elapsed	Exit	Granted	…	Name
scc1	0.0	0.0	0.0	1	0.0	…	SCC1_0004175_MyoD1-C_0002_1	…

Adri
----------------------------------------
[Edit 1 times, last edit by adriverhoef at May 15, 2023 9:44:36 PM]
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adriverhoef
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
And there are the next ones:
workunit 298014674
SCC1_0004175_MyoD1-C_0903_0  Linuxmint     Error  2023-05-15T21:07:50  2023-05-15T21:33:13    0.00/0.00
SCC1_0004175_MyoD1-C_0903_1  Linux Arch    InPrg  2023-05-15T21:08:00  2023-05-21T21:08:00    0.00/0.00
SCC1_0004175_MyoD1-C_0903_2  Fedora Linux  Error  2023-05-15T21:33:26  2023-05-15T21:35:34    0.00/0.00
SCC1_0004175_MyoD1-C_0903_3  Linux Ubuntu  Error  2023-05-15T21:35:55  2023-05-15T21:38:03    0.00/0.00 
SCC1_0004175_MyoD1-C_0903_4  Linux Ubuntu  InPrg  2023-05-15T21:38:14  2023-05-18T21:38:14    0.00/0.00

workunit 298016961
SCC1_0004175_MyoD1-C_1379_0  Linux Ubuntu  Error  2023-05-15T21:37:01  2023-05-15T22:47:54    0.00/0.00
SCC1_0004175_MyoD1-C_1379_1  Linux Debian  Error  2023-05-15T21:37:05  2023-05-15T21:39:09    0.00/0.00
SCC1_0004175_MyoD1-C_1379_2  Linux Debian  Error  2023-05-15T21:39:13  2023-05-15T21:43:45    0.00/0.00
SCC1_0004175_MyoD1-C_1379_3  Linux         InPrg  2023-05-15T21:43:51  2023-05-18T21:43:51    0.00/0.00
SCC1_0004175_MyoD1-C_1379_4  Fedora Linux  Error  2023-05-15T22:47:58  2023-05-15T22:50:05    0.00/0.00

----------------------------------------
[Edit 1 times, last edit by adriverhoef at May 15, 2023 11:07:58 PM]
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AgrFan
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
SCC1_0004175_MyoD1-C_1461_1

<core_client_version>7.14.3</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.
[20:58:19] Number of tasks = 1
[20:58:19] Running task 0,CPU time at start of task 0 was 0.000000
[20:58:19] ./cmpd-1001461.pdbqt size = 24 6 ../../projects/www.worldcommunitygrid.org/scc1.MyoD1-C.pdbqt size = 1268 0

Parse error on line 190 in file "..\..\projects\www.worldcommunitygrid.org\5bc9923e3e0de4adcfcb067d7638c429.pdbqt": ATOM syntax incorrect: "62 " is not a valid atom number
VINA failed. rc = 1. Exiting

</stderr_txt>
]]>

https://www.worldcommunitygrid.org/contribution/workunit/298017294
----------------------------------------
[Edit 1 times, last edit by AgrFan at May 16, 2023 1:11:19 AM]
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TPCBF
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
Haven't checked the actual WU logs, but I noticed a bunch of _2 WUs, on various hosts, that immediately crap out with a "Computation error".

Those that I noticed where all on Windows 10, i7 CPUs with at least 16GB of RAM....

Ralf
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alanb1951
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
The flex file for MyoD1-C is indeed invalid -- I managed to find one that hadn't failed yet, and had a look at the data files; that particular line is missing a space between the ATOM keyword and the actual atom number, hence the specific message! The rest of the file seems valid (as far as I can tell...)

The rigid part of the receptor is in a "sticky" file, but the flex file is downloaded anew for each job -- I don't know if it ever changes between jobs, though...

Looks like these will have to be fixed, repackaged and fed through again :-)

Cheers - Al.
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TPCBF
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
Just had also a _0 and a _1 WU fail, also with that same error message.

Seems like a bad batch

SCC1_0004175_MyoD1-C_5893_0 (Quorum 2)
SCC1_0004175_MyoD1-C_0247_1 (Quorum 1)
SCC1_0004175_MyoD1-C_4933_2 (Quorum 2)
SCC1_0004175_MyoD1-C_4948_2 (Quorum 2)
SCC1_0004175_MyoD1-C_3171_2 (Quorum 2)


Ralf
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bfmorse
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
I have about 40 62+ different WU's with that error as well. Be interesting to see what the feedback is.

See my email for more details:
Computer name "DESKTOP" - 6 cores 12 processes
Computer name "WCGabcc" - (a=# cores) (b=Cpu -or- Gpu equipt) (cc=# of processes)

1: ETA - ref to email, added ref info to computer names and update quantity
2: ETA - Added "+" to 62
----------------------------------------
[Edit 2 times, last edit by bfmorse at May 16, 2023 6:46:51 AM]
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Crystal Pellet
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
I got a resend SCC1_0004175_MyoD1-C_7039_3 and saw that the workunit already had _0 and _1 error returned.
I pushed my task to run directly and indeed: computation error. https://www.worldcommunitygrid.org/contribution/workunit/298044341

Parse error on line 190 in file "..\..\projects\www.worldcommunitygrid.org\5b1bb218f9f633ed857311c7765db534.pdbqt": ATOM syntax incorrect: "62 " is not a valid atom number
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adriverhoef
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
The errors are piling up and it is difficult to receive any new tasks, whether it be ARP1, MCM1 or SCC1; coincidence or not?

workunit 298028773   workunit 298012800   workunit 298039727   workunit 298030538   workunit 298015579
workunit 298028774   workunit 298029806   workunit 298029321   workunit 298021233   workunit 298029094
workunit 298021343   workunit 298030818   workunit 298012570   workunit 298049235   workunit 298043646

When I woke up I was just in time to observe one task getting "Aborted by project" in BOINC Manager:
workunit 298025869

I have received three '.pdbqt'-files at 23:34 last night, one of which is the 'mother' (scc1.MyoD1-C.pdbqt):
$ ls -l *.pdbqt | grep 23:34
-rw-r--r--. 1 boinc boinc   9297 May 15 23:34 36c67ce04661ed055563c95480c09549.pdbqt
-rw-r--r--. 1 boinc boinc   9297 May 15 23:34 f8163ee25647523ac5a95221d48429c8.pdbqt
-rw-r--r--. 1 boinc boinc 102811 May 15 23:34 scc1.MyoD1-C.pdbqt

They are still in my queue:
$ wcgresults -ND | grep 23:34
Sun May 21 23:34:00 2023	SCC1_0004175_MyoD1-C_1334_0
Sun May 21 23:34:00 2023	SCC1_0004175_MyoD1-C_1326_0

When I compare the two 'child' .pdbqt files, they are the same:
$ diff f8163ee25647523ac5a95221d48429c8.pdbqt 36c67ce04661ed055563c95480c09549.pdbqt | wc -l
0

Oops, my queue is getting empty, while typing this they were next, so they are gone now. But I still have:

$ ls -l *.pdbqt | grep 04:00
-rw-r--r--. 1 boinc boinc   9297 May 16 04:00 7e83e397db0c9c1c5e84186e35174f68.pdbqt
-rw-r--r--. 1 boinc boinc   9297 May 16 04:00 d5de000bd273c5d6a09a3df3e01dc0d0.pdbqt


alanb1951 / Al:
Incredible what one missing space can do!
$ grep -h ^ATOM 7e83e397db0c9c1c5e84186e35174f68.pdbqt | grep -C 3 "^ATOM  *62 "
ATOM     59  ND2 ASN D 126     103.474 -21.554  10.753  1.00 38.70    -0.369 N 
ATOM     60 2HD2 ASN D 126     104.039 -21.222   9.971  1.00  0.00     0.159 HD
ATOM     61 1HD2 ASN D 126     103.874 -22.157  11.472  1.00  0.00     0.159 HD
ATOM    62  CA  LYS D 146     104.561 -27.328   6.174  1.00 24.50     0.159 C 
ATOM     63  CB  LYS D 146     104.118 -25.898   5.881  1.00 24.78     0.032 C 
ATOM     64  CG  LYS D 146     104.249 -24.933   7.049  1.00 27.17     0.004 C 
ATOM     65  CD  LYS D 146     103.806 -23.544   6.607  1.00 28.42     0.032 C


Adri
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adriverhoef
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Re: [Error] ATOM syntax incorrect: "62 " is not a valid atom number
I am trying a hot fix on the *.pdbqt files by applying this:
# grep -l ^ATOM"    62 " *.pdbqt && echo HOT FIX && sed -i 's/^ATOM    62 /ATOM     62 /' $(grep -l ^ATOM"    62 " *.pdbqt)

Yes, it works!
$ wcgresults -NCORPSED | egrep "^D|MyoD1-C"
Deadline----------------	CPUtime 	Remaining	Est.Left	Percentage	Status	slOt	Name----------------
Mon May 22 06:23:15 2023	 0:10:16	 0:49:18	 0:49:10	 17.2923%	(R)	  12	SCC1_0004175_MyoD1-C_6994_0
Mon May 22 06:27:31 2023	 0:00:45	 0:58:54	        	  1.1997%	(R)	  24	SCC1_0004175_MyoD1-C_7070_1
Mon May 22 08:46:49 2023	 0:00:45	 0:58:36	        	  1.6998%	(R)	  28	SCC1_0004175_MyoD1-C_9983_1
Mon May 22 09:59:02 2023	 0:00:45	 0:58:40	        	  1.5986%	(R)	  29	SCC1_0004175_MyoD1-C_11307_1
Mon May 22 09:59:02 2023	 0:00:45	 0:58:47	        	  1.3997%	(R)	  30	SCC1_0004175_MyoD1-C_11306_1
Mon May 22 10:19:38 2023	 0:00:45	 0:58:36	        	  1.6997%	(R)	  31	SCC1_0004175_MyoD1-C_11660_1
Mon May 22 10:19:38 2023	 0:00:45	 0:58:36	        	  1.6995%	(R)	  33	SCC1_0004175_MyoD1-C_11652_0
Mon May 22 11:06:51 2023	 0:00:45	 0:58:32	        	  1.7984%	(R)	  34	SCC1_0004175_MyoD1-C_12536_1
Mon May 22 11:22:07 2023	 0:00:36	 0:58:50	        	  1.3000%	(R)	  37	SCC1_0004175_MyoD1-C_12742_0

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[Edit 3 times, last edit by adriverhoef at May 16, 2023 9:50:54 AM]
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