Task 10781

Name testsim_32269_1550386145.719317_1
Workunit 3982
Created 17 Feb 2019, 6:49:09 UTC
Sent 17 Feb 2019, 6:49:22 UTC
Report deadline 24 Feb 2019, 6:49:22 UTC
Received 19 Feb 2019, 3:30:10 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 61
Run time 1 min 13 sec
CPU time
Validate state Valid
Credit 19.57
Device peak FLOPS 116.16 GFLOPS
Application version testsim v1.00 (vbox64_mt)
windows_x86_64
Peak working set size 85.52 MB
Peak swap size 95.89 MB
Peak disk usage 203.57 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-02-18 22:28:49 (5736): vboxwrapper (7.9.26200): starting
2019-02-18 22:28:49 (5736): Feature: Checkpoint interval offset (343 seconds)
2019-02-18 22:28:49 (5736): Detected: VirtualBox COM Interface (Version: 5.2.26)
2019-02-18 22:28:49 (5736): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-02-18 22:28:49 (5736): Create VM. (boinc_b68b373d2b3f887a, slot#28)
2019-02-18 22:28:49 (5736): Updating drive controller type and model for desired configuration.
2019-02-18 22:28:49 (5736): Setting Memory Size for VM. (2363MB)
2019-02-18 22:28:49 (5736): Setting CPU Count for VM. (1)
2019-02-18 22:28:49 (5736): Setting Chipset Options for VM.
2019-02-18 22:28:49 (5736): Setting Boot Options for VM.
2019-02-18 22:28:49 (5736): Enabling VM Network Access.
2019-02-18 22:28:49 (5736): Setting Network Configuration for NAT.
2019-02-18 22:28:49 (5736): Disabling USB Support for VM.
2019-02-18 22:28:49 (5736): Disabling COM Port Support for VM.
2019-02-18 22:28:49 (5736): Disabling LPT Port Support for VM.
2019-02-18 22:28:49 (5736): Disabling Audio Support for VM.
2019-02-18 22:28:49 (5736): Disabling Clipboard Support for VM.
2019-02-18 22:28:49 (5736): Disabling Drag and Drop Support for VM.
2019-02-18 22:28:49 (5736): Adding storage controller(s) to VM.
2019-02-18 22:28:49 (5736): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-02-18 22:28:49 (5736): Adding VirtualBox Guest Additions to VM.
2019-02-18 22:28:49 (5736): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-02-18 22:28:49 (5736): Enabling shared directory for VM.
2019-02-18 22:28:49 (5736): Starting VM. (boinc_b68b373d2b3f887a, slot#28)
2019-02-18 22:28:58 (5736): Guest Log: BIOS: VirtualBox 5.2.26

2019-02-18 22:28:58 (5736): Guest Log: CPUID EDX: 0x078bfbff

2019-02-18 22:28:58 (5736): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-02-18 22:28:58 (5736): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-02-18 22:28:58 (5736): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-02-18 22:28:58 (5736): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-02-18 22:28:58 (5736): Guest Log: BIOS: Booting from CD-ROM...

2019-02-18 22:28:58 (5736): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-02-18 22:28:58 (5736): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-02-18 22:28:58 (5736): Successfully started VM. (PID = '12808')
2019-02-18 22:28:58 (5736): Reporting VM Process ID to BOINC.
2019-02-18 22:29:03 (5736): VM state change detected. (old = 'poweroff', new = 'running')
2019-02-18 22:29:08 (5736): Guest Log: net.ipv4.ip_forward = 1

2019-02-18 22:29:08 (5736): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-02-18 22:29:08 (5736): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-02-18 22:29:08 (5736): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-02-18 22:29:08 (5736): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-02-18 22:29:08 (5736): Guest Log: Segmentation fault

2019-02-18 22:29:08 (5736): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-02-18 22:29:08 (5736): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-02-18 22:29:08 (5736): Guest Log: automount ...

2019-02-18 22:29:08 (5736): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-02-18 22:29:08 (5736): Guest Log: automount over.

2019-02-18 22:29:08 (5736): Guest Log: Setting hostname to boot2docker Done.

2019-02-18 22:29:08 (5736): Guest Log: Mon Feb 18 22:29:06 UTC 2019 dhcp -------------------------------

2019-02-18 22:29:13 (5736): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1072)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00 (1304)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:00 (1305)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00 (1306)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0 (1307)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0/event0 (1308)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00 (1309)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1 (1310)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1/event1 (1311)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00 (1312)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00 (1313)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00 (1314)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00/power_supply/AC (1315)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00 (1316)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/device:01 (1317)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6 (1318)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6/event5 (1319)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:00 (1320)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:01 (1321)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:00 (1322)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:01 (1323)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:02 (1324)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:03 (1325)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C02:00 (1326)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00 (1327)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00/power_supply/BAT0 (1328)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP8390:00 (1329)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00 (1330)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1331)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1332)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1333)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1334)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1335)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1336)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1337)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1338)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1339)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:02 (1340)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1341)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:01 (1342)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:02 (1343)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1344)

2019-02-18 22:29:13 (5736): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:01 (1345)

2019-02-18 22:29:13 (5736): Preference change detected
2019-02-18 22:29:13 (5736): Setting CPU throttle for VM. (100%)
2019-02-18 22:29:13 (5736): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 300 seconds) or (Vbox_job.xml: 600 seconds))
2019-02-18 22:29:18 (5736): Guest Log: Mon Feb 18 22:29:12 UTC 2019 dhcp -------------------------------

2019-02-18 22:29:18 (5736): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.000181 main     Log opened 2019-02-18T22:29:12.847213000Z

2019-02-18 22:29:18 (5736): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.000181 main     Log opened 2019-02-18T22:29:12.847213000Z

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008296 main     OS Product: Linux

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008515 main     OS Release: 4.1.19-boot2docker

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008562 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008296 main     OS Product: Linux

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008515 main  00:00:00.012846 main     Executable: /sbin/VBoxService

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.012855 main     Process ID: 834

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.012857 main     Package type: LINUX_64BITS_GENERIC

2019-02-18 22:29:18 (5736): Guest Log:    OS Release: 4.1.19-boot2docker

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.008562 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.012846 main     Executable: /sbin/VBoxService

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.012855 main     Process ID: 834

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.012857 main     Package type: LINUX_64BITS_GENERIC

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.022680 main     5.0.16 r105871 started. Verbose level = 0

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.028251 vminfo   rtldrNativeLoad: dlopen('libdbus-1.so.3', RTLD_NOW | RTLD_LOCAL) failed: libdbus-1.so.3: cannot open shared object file: No such file or directory

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.028436 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-02-18 22:29:18 (5736): Guest Log: 00:00:00.022680 main     5.0.16 r105871 started. Verbose level = 0

2019-02-18 22:29:18 (5736): Guest Log: Mounting BOINC shared/...

2019-02-18 22:29:18 (5736): Guest Log: -------------------

2019-02-18 22:29:18 (5736): Guest Log: Tue Feb 19 03:29:14 UTC 2019

2019-02-18 22:29:23 (5736): Guest Log: 00:00:05.030110 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-02-18 22:29:23 (5736): Guest Log: Tue Feb 19 03:29:19 UTC 2019

2019-02-18 22:29:23 (5736): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-02-18 22:29:23 (5736): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-02-18 22:29:23 (5736): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-02-18 22:29:23 (5736): Guest Log:        valid_lft forever preferred_lft forever

2019-02-18 22:29:23 (5736): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-02-18 22:29:23 (5736): Guest Log:     link/ether 9e:9c:28:29:e5:06 brd ff:ff:ff:ff:ff:ff

2019-02-18 22:29:23 (5736): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-02-18 22:29:23 (5736): Guest Log:     link/ether 08:00:27:7b:5d:6e brd ff:ff:ff:ff:ff:ff

2019-02-18 22:29:23 (5736): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-02-18 22:29:23 (5736): Guest Log:        valid_lft forever preferred_lft forever

2019-02-18 22:29:23 (5736): Guest Log: -------------------

2019-02-18 22:29:23 (5736): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-02-18 22:29:23 (5736): Guest Log: Waiting for Docker daemon to start...

2019-02-18 22:29:23 (5736): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-02-18 22:29:23 (5736): Guest Log: Running boinc_app...

2019-02-18 22:29:23 (5736): Guest Log: Importing Docker image from BOINC...

2019-02-18 22:29:28 (5736): Guest Log: 00:00:10.031966 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-02-18 22:29:43 (5736): Guest Log: Prerun diagnostics...

2019-02-18 22:29:43 (5736): Guest Log: REPOSITORY              TAG                 IMAGE ID            CREATED             SIZE

2019-02-18 22:29:43 (5736): Guest Log: claughton/gromacs2018   latest              af5cb836fee4        9 months ago        465.8 MB

2019-02-18 22:29:43 (5736): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-02-18 22:29:43 (5736): Guest Log: 474.2M	/var/lib/docker

2019-02-18 22:29:43 (5736): Guest Log:               total        used        free      shared  buff/cache   available

2019-02-18 22:29:43 (5736): Guest Log: Mem:           2308          47        1584         638         675        1587

2019-02-18 22:29:43 (5736): Guest Log: Swap:           526           0         526

2019-02-18 22:29:43 (5736): Guest Log: Prerun commands...

2019-02-18 22:29:43 (5736): Guest Log: Running... 

2019-02-18 22:29:48 (5736): Guest Log:                       :-) GROMACS - gmx pdb2gmx, 2018 (-:

2019-02-18 22:29:48 (5736): Guest Log:                             GROMACS is written by:

2019-02-18 22:29:48 (5736): Guest Log:      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   

2019-02-18 22:29:48 (5736): Guest Log:  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  

2019-02-18 22:29:48 (5736): Guest Log:  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis

2019-02-18 22:29:48 (5736): Guest Log:     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    

2019-02-18 22:29:48 (5736): Guest Log:   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 

2019-02-18 22:29:48 (5736): Guest Log:    Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   

2019-02-18 22:29:48 (5736): Guest Log:    Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  

2019-02-18 22:29:48 (5736): Guest Log:    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   

2019-02-18 22:29:48 (5736): Guest Log:                            and the project leaders:

2019-02-18 22:29:48 (5736): Guest Log:         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

2019-02-18 22:29:48 (5736): Guest Log: Copyright (c) 1991-2000, University of Groningen, The Netherlands.

2019-02-18 22:29:48 (5736): Guest Log: Copyright (c) 2001-2017, The GROMACS development team at

2019-02-18 22:29:48 (5736): Guest Log: Uppsala University, Stockholm University and

2019-02-18 22:29:48 (5736): Guest Log: the Royal Institute of Technology, Sweden.

2019-02-18 22:29:48 (5736): Guest Log: check out http://www.gromacs.org for more information.

2019-02-18 22:29:48 (5736): Guest Log: GROMACS is free software; you can redistribute it and/or modify it

2019-02-18 22:29:48 (5736): Guest Log: under the terms of the GNU Lesser General Public License

2019-02-18 22:29:48 (5736): Guest Log: as published by the Free Software Foundation; either version 2.1

2019-02-18 22:29:48 (5736): Guest Log: of the License, or (at your option) any later version.

2019-02-18 22:29:48 (5736): Guest Log: GROMACS:      gmx pdb2gmx, version 2018

2019-02-18 22:29:48 (5736): Guest Log: Executable:   /opt/gromacs/sse2/bin/gmx

2019-02-18 22:29:48 (5736): Guest Log: Data prefix:  /opt/gromacs/sse2

2019-02-18 22:29:48 (5736): Guest Log: Working dir:  /

2019-02-18 22:29:48 (5736): Guest Log: Command line:

2019-02-18 22:29:48 (5736): Guest Log:   gmx pdb2gmx -f /root/shared/E2Bwt.pdb -o /root/shared/results/E2Bwt.gro -p /root/shared/results/E2Bwt.top -ignh -ff gromos53a6 -water spc

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/aminoacids.r2b

2019-02-18 22:29:48 (5736): Guest Log: All occupancies are one

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/atomtypes.atp

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 1

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 2

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 3

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2019-02-18 22:29:48 (5736): Guest Log: Atomtype 34

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 35

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 36

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 37

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 38

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 39

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 40

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 41

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 42

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 43

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 44

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 45

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 46

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 47

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 48

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 49

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 50

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 51

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 52

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 53

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 54

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 55

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 56

2019-02-18 22:29:48 (5736): Guest Log: Atomtype 57

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/aminoacids.rtp

2019-02-18 22:29:48 (5736): Guest Log: Using default: not generating all possible dihedrals

2019-02-18 22:29:48 (5736): Guest Log: Using default: excluding 3 bonded neighbors

2019-02-18 22:29:48 (5736): Guest Log: Using default: generating 1,4 H--H interactions

2019-02-18 22:29:48 (5736): Guest Log: Using default: removing proper dihedrals found on the same bond as a proper dihedral

2019-02-18 22:29:48 (5736): Guest Log: Residue 1

2019-02-18 22:29:48 (5736): Guest Log: Residue 2

2019-02-18 22:29:48 (5736): Guest Log: Residue 3

2019-02-18 22:29:48 (5736): Guest Log: Residue 4

2019-02-18 22:29:48 (5736): Guest Log: Residue 5

2019-02-18 22:29:48 (5736): Guest Log: Residue 6

2019-02-18 22:29:48 (5736): Guest Log: Residue 7

2019-02-18 22:29:48 (5736): Guest Log: Residue 8

2019-02-18 22:29:48 (5736): Guest Log: Residue 9

2019-02-18 22:29:48 (5736): Guest Log: Residue 10

2019-02-18 22:29:48 (5736): Guest Log: Residue 11

2019-02-18 22:29:48 (5736): Guest Log: Residue 12

2019-02-18 22:29:48 (5736): Guest Log: Residue 13

2019-02-18 22:29:48 (5736): Guest Log: Residue 14

2019-02-18 22:29:48 (5736): Guest Log: Residue 15

2019-02-18 22:29:48 (5736): Guest Log: Residue 16

2019-02-18 22:29:48 (5736): Guest Log: Residue 17

2019-02-18 22:29:48 (5736): Guest Log: Residue 18

2019-02-18 22:29:48 (5736): Guest Log: Residue 19

2019-02-18 22:29:48 (5736): Guest Log: Residue 20

2019-02-18 22:29:48 (5736): Guest Log: Residue 21

2019-02-18 22:29:48 (5736): Guest Log: Residue 22

2019-02-18 22:29:48 (5736): Guest Log: Residue 23

2019-02-18 22:29:48 (5736): Guest Log: Residue 24

2019-02-18 22:29:48 (5736): Guest Log: Residue 25

2019-02-18 22:29:48 (5736): Guest Log: Residue 26

2019-02-18 22:29:48 (5736): Guest Log: Residue 27

2019-02-18 22:29:48 (5736): Guest Log: Residue 28

2019-02-18 22:29:48 (5736): Guest Log: Residue 29

2019-02-18 22:29:48 (5736): Guest Log: Residue 30

2019-02-18 22:29:48 (5736): Guest Log: Residue 31

2019-02-18 22:29:48 (5736): Guest Log: Residue 32

2019-02-18 22:29:48 (5736): Guest Log: Residue 33

2019-02-18 22:29:48 (5736): Guest Log: Residue 34

2019-02-18 22:29:48 (5736): Guest Log: Residue 35

2019-02-18 22:29:48 (5736): Guest Log: Residue 36

2019-02-18 22:29:48 (5736): Guest Log: Residue 37

2019-02-18 22:29:48 (5736): Guest Log: Residue 38

2019-02-18 22:29:48 (5736): Guest Log: Residue 39

2019-02-18 22:29:48 (5736): Guest Log: Residue 40

2019-02-18 22:29:48 (5736): Guest Log: Residue 41

2019-02-18 22:29:48 (5736): Guest Log: Residue 42

2019-02-18 22:29:48 (5736): Guest Log: Residue 43

2019-02-18 22:29:48 (5736): Guest Log: Residue 44

2019-02-18 22:29:48 (5736): Guest Log: Residue 45

2019-02-18 22:29:48 (5736): Guest Log: Residue 46

2019-02-18 22:29:48 (5736): Guest Log: Residue 47

2019-02-18 22:29:48 (5736): Guest Log: Residue 48

2019-02-18 22:29:48 (5736): Guest Log: Residue 49

2019-02-18 22:29:48 (5736): Guest Log: Residue 50

2019-02-18 22:29:48 (5736): Guest Log: Residue 51

2019-02-18 22:29:48 (5736): Guest Log: Residue 52

2019-02-18 22:29:48 (5736): Guest Log: Residue 53

2019-02-18 22:29:48 (5736): Guest Log: Residue 54

2019-02-18 22:29:48 (5736): Guest Log: Residue 55

2019-02-18 22:29:48 (5736): Guest Log: Residue 56

2019-02-18 22:29:48 (5736): Guest Log: Residue 57

2019-02-18 22:29:48 (5736): Guest Log: Residue 58

2019-02-18 22:29:48 (5736): Guest Log: Residue 59

2019-02-18 22:29:48 (5736): Guest Log: Residue 60

2019-02-18 22:29:48 (5736): Guest Log: Residue 61

2019-02-18 22:29:48 (5736): Guest Log: Residue 62

2019-02-18 22:29:48 (5736): Guest Log: Residue 63

2019-02-18 22:29:48 (5736): Guest Log: Residue 64

2019-02-18 22:29:48 (5736): Guest Log: Residue 65

2019-02-18 22:29:48 (5736): Guest Log: Residue 66

2019-02-18 22:29:48 (5736): Guest Log: Residue 67

2019-02-18 22:29:48 (5736): Guest Log: Residue 68

2019-02-18 22:29:48 (5736): Guest Log: Residue 69

2019-02-18 22:29:48 (5736): Guest Log: Residue 70

2019-02-18 22:29:48 (5736): Guest Log: Residue 71

2019-02-18 22:29:48 (5736): Guest Log: Residue 72

2019-02-18 22:29:48 (5736): Guest Log: Residue 73

2019-02-18 22:29:48 (5736): Guest Log: Residue 74

2019-02-18 22:29:48 (5736): Guest Log: Residue 75

2019-02-18 22:29:48 (5736): Guest Log: Residue 76

2019-02-18 22:29:48 (5736): Guest Log: Residue 77

2019-02-18 22:29:48 (5736): Guest Log: Residue 78

2019-02-18 22:29:48 (5736): Guest Log: Residue 79

2019-02-18 22:29:48 (5736): Guest Log: Residue 80

2019-02-18 22:29:48 (5736): Guest Log: Residue 81

2019-02-18 22:29:48 (5736): Guest Log: Residue 82

2019-02-18 22:29:48 (5736): Guest Log: Residue 83

2019-02-18 22:29:48 (5736): Guest Log: Residue 84

2019-02-18 22:29:48 (5736): Guest Log: Residue 85

2019-02-18 22:29:48 (5736): Guest Log: Residue 86

2019-02-18 22:29:48 (5736): Guest Log: Residue 87

2019-02-18 22:29:48 (5736): Guest Log: Residue 88

2019-02-18 22:29:48 (5736): Guest Log: Residue 89

2019-02-18 22:29:48 (5736): Guest Log: Residue 90

2019-02-18 22:29:48 (5736): Guest Log: Residue 91

2019-02-18 22:29:48 (5736): Guest Log: Residue 92

2019-02-18 22:29:48 (5736): Guest Log: Residue 93

2019-02-18 22:29:48 (5736): Guest Log: Residue 94

2019-02-18 22:29:48 (5736): Guest Log: Residue 95

2019-02-18 22:29:48 (5736): Guest Log: Residue 96

2019-02-18 22:29:48 (5736): Guest Log: Residue 97

2019-02-18 22:29:48 (5736): Guest Log: Residue 98

2019-02-18 22:29:48 (5736): Guest Log: Residue 99

2019-02-18 22:29:48 (5736): Guest Log: Residue 100

2019-02-18 22:29:48 (5736): Guest Log: Residue 101

2019-02-18 22:29:48 (5736): Guest Log: Residue 102

2019-02-18 22:29:48 (5736): Guest Log: Residue 103

2019-02-18 22:29:48 (5736): Guest Log: Residue 104

2019-02-18 22:29:48 (5736): Guest Log: Residue 105

2019-02-18 22:29:48 (5736): Guest Log: Residue 106

2019-02-18 22:29:48 (5736): Guest Log: Residue 107

2019-02-18 22:29:48 (5736): Guest Log: Residue 108

2019-02-18 22:29:48 (5736): Guest Log: Sorting it all out...

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/aminoacids.hdb

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb

2019-02-18 22:29:48 (5736): Guest Log: Opening force field file /opt/gromacs/sse2/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb

2019-02-18 22:29:48 (5736): Guest Log: Analysing hydrogen-bonding network for automated assignment of histidine

2019-02-18 22:29:48 (5736): Guest Log:  protonation. 228 donors and 217 acceptors were found.

2019-02-18 22:29:48 (5736): Guest Log: There are 323 hydrogen bonds

2019-02-18 22:29:48 (5736): Guest Log: Will use HISE for residue 75

2019-02-18 22:29:48 (5736): Guest Log: Will use HISD for residue 134

2019-02-18 22:29:48 (5736): Guest Log: 8 out of 8 lines of specbond.dat converted successfully

2019-02-18 22:29:48 (5736): Guest Log: Special Atom Distance matrix:

2019-02-18 22:29:48 (5736): Guest Log:                    CYS21   HIS75   CYS76   CYS85  CYS107  CYS113  MET128

2019-02-18 22:29:48 (5736): Guest Log:                    SG167  NE2603   SG609   SG673   SG843   SG886   SD994

2019-02-18 22:29:48 (5736): Guest Log:    HIS75  NE2603   1.449

2019-02-18 22:29:48 (5736): Guest Log:    CYS76   SG609   1.995   0.569

2019-02-18 22:29:48 (5736): Guest Log:    CYS85   SG673   1.933   1.013   0.869

2019-02-18 22:29:48 (5736): Guest Log:   CYS107   SG843   0.463   1.088   1.637   1.704

2019-02-18 22:29:48 (5736): Guest Log:   CYS113   SG886   1.900   0.510   0.368   1.125   1.492

2019-02-18 22:29:48 (5736): Guest Log:   MET128   SD994   2.585   1.219   0.818   1.508   2.158   0.712

2019-02-18 22:29:48 (5736): Guest Log:   HIS134 NE21045   2.070   0.709   0.593   1.427   1.698   0.524   0.912

2019-02-18 22:29:48 (5736): Guest Log:   MET137  SD1071   2.618   1.432   1.290   1.994   2.328   1.359   1.549

2019-02-18 22:29:48 (5736): Guest Log:                   HIS134

2019-02-18 22:29:48 (5736): Guest Log:                  NE21045

2019-02-18 22:29:48 (5736): Guest Log:   MET137  SD1071   0.849

2019-02-18 22:29:48 (5736): Guest Log: Making bonds...

2019-02-18 22:29:48 (5736): Guest Log: Number of bonds was 1530, now 1525

2019-02-18 22:29:48 (5736): Guest Log: Generating angles, dihedrals and pairs...

2019-02-18 22:29:48 (5736): Guest Log: WARNING: WARNING: Residue 1 named SER of a molecule in the input file was mapped

2019-02-18 22:29:48 (5736): Guest Log: to an entry in the topology database, but the atom H used in

2019-02-18 22:29:48 (5736): Guest Log: an interaction of type angle in that entry is not found in the

2019-02-18 22:29:48 (5736): Guest Log: input file. Perhaps your atom and/or residue naming needs to be

2019-02-18 22:29:48 (5736): Guest Log: fixed.

2019-02-18 22:29:48 (5736): Guest Log: WARNING: WARNING: Residue 148 named THR of a molecule in the input file was mapped

2019-02-18 22:29:48 (5736): Guest Log: to an entry in the topology database, but the atom O used in

2019-02-18 22:29:48 (5736): Guest Log: an interaction of type angle in that entry is not found in the

2019-02-18 22:29:48 (5736): Guest Log: input file. Perhaps your atom and/or residue naming needs to be

2019-02-18 22:29:48 (5736): Guest Log: fixed.

2019-02-18 22:29:48 (5736): Guest Log: Before cleaning: 2467 pairs

2019-02-18 22:29:48 (5736): Guest Log: Before cleaning: 2948 dihedrals

2019-02-18 22:29:48 (5736): Guest Log: Making cmap torsions...

2019-02-18 22:29:48 (5736): Guest Log: There are  817 dihedrals,  755 impropers, 2229 angles

2019-02-18 22:29:48 (5736): Guest Log:           2467 pairs,     1525 bonds and     0 virtual sites

2019-02-18 22:29:48 (5736): Guest Log: Total mass 16541.020 a.m.u.

2019-02-18 22:29:48 (5736): Guest Log: Total charge 2.000 e

2019-02-18 22:29:48 (5736): Guest Log: Writing topology

2019-02-18 22:29:48 (5736): Guest Log: Writing coordinate file...

2019-02-18 22:29:48 (5736): Guest Log: GROMACS reminds you: "We Don't Bother Anyone" (LIVE)

2019-02-18 22:29:48 (5736): Guest Log: Using the Gromos53a6 force field in directory gromos53a6.ff

2019-02-18 22:29:48 (5736): Guest Log: Reading /root/shared/E2Bwt.pdb...

2019-02-18 22:29:48 (5736): Guest Log: Read 1162 atoms

2019-02-18 22:29:48 (5736): Guest Log: Analyzing pdb file

2019-02-18 22:29:48 (5736): Guest Log: Splitting chemical chains based on TER records or chain id changing.

2019-02-18 22:29:48 (5736): Guest Log: There are 1 chains and 0 blocks of water and 148 residues with 1162 atoms

2019-02-18 22:29:48 (5736): Guest Log:   chain  #res #atoms

2019-02-18 22:29:48 (5736): Guest Log:   1 'A'   148   1162  

2019-02-18 22:29:48 (5736): Guest Log: Reading residue database... (gromos53a6)

2019-02-18 22:29:48 (5736): Guest Log: Processing chain 1 'A' (1162 atoms, 148 residues)

2019-02-18 22:29:48 (5736): Guest Log: Identified residue SER0 as a starting terminus.

2019-02-18 22:29:48 (5736): Guest Log: Identified residue THR147 as a ending terminus.

2019-02-18 22:29:48 (5736): Guest Log: Start terminus SER-0: NH3+

2019-02-18 22:29:48 (5736): Guest Log: End terminus THR-147: COO-

2019-02-18 22:29:48 (5736): Guest Log: Checking for duplicate atoms....

2019-02-18 22:29:48 (5736): Guest Log: Generating any missing hydrogen atoms and/or adding termini.

2019-02-18 22:29:48 (5736): Guest Log: Now there are 148 residues with 1494 atoms

2019-02-18 22:29:48 (5736): Guest Log: 		--------- PLEASE NOTE ------------

2019-02-18 22:29:48 (5736): Guest Log: You have successfully generated a topology from: /root/shared/E2Bwt.pdb.

2019-02-18 22:29:48 (5736): Guest Log: The Gromos53a6 force field and the spc water model are used.

2019-02-18 22:29:48 (5736): Guest Log: 		--------- ETON ESAELP ------------

2019-02-18 22:29:48 (5736): Guest Log: Postrun commands...

2019-02-18 22:29:48 (5736): Guest Log: boinc_app exited (0)

2019-02-18 22:29:48 (5736): Guest Log: Saving results...

2019-02-18 22:29:48 (5736): Guest Log: E2Bwt.gro

2019-02-18 22:29:48 (5736): Guest Log: E2Bwt.top

2019-02-18 22:29:48 (5736): VM Completion File Detected.
2019-02-18 22:29:48 (5736): Powering off VM.
2019-02-18 22:29:49 (5736): Successfully stopped VM.
2019-02-18 22:29:54 (5736): Deregistering VM. (boinc_b68b373d2b3f887a, slot#28)
2019-02-18 22:29:54 (5736): Removing virtual disk drive(s) from VM.
2019-02-18 22:29:54 (5736): Removing network bandwidth throttle group from VM.
2019-02-18 22:29:54 (5736): Removing storage controller(s) from VM.
2019-02-18 22:29:54 (5736): Removing VM from VirtualBox.
22:29:59 (5736): called boinc_finish(0)

</stderr_txt>
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©2019 GPCR Drug Discovery group at the Pompeu Fabra University