[Dock-fans] DOCK3.5 score "aborted core"

Scott Brozell sbrozell at scripps.edu
Thu Sep 13 16:03:59 PDT 2007


Hi,

What version of DOCK did you use ?
What were the results from the install/test/chemgrid_generation
and install/test/chemgrid_score tests ?

thanks,
Scott

On Wed, 12 Sep 2007, BA S wrote:

> I am having trouble docking a ligand utilizing DOCK3.5 scoring. I get
> the following error.
>
> Initializing Library File Routines...
> Initializing Orienting Routines...
> Initializing Bump Filter Routines...
>  Reading the bump grid from chem52.bmp
> Initializing Dock3.5 Score Routines...
>  Reading chemgrids from chem52.cmg
>  Reading DelPhi grid from chem52.phi
>
> -----------------------------------
> Elapsed time for docking:      217 seconds
>
>  Anchors:               1
>  Orientations:          1000
>  Conformations:         1000
>
>  Energy Score:        -6696.385742
>           vdw:        -6696.385742
>            es:            0.000000
>
> 1 Molecules Processed
> Total elapsed time:     217 seconds
> *** glibc detected *** ./dock6: double free or corruption (!prev):
> 0x08182080 ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6[0xb7d947cd]
> /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7d97e30]
> /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7f56d11]
> /usr/lib/libstdc++.so.6(_ZdaPv+0x1d)[0xb7f56d6d]
> ./dock6[0x805776f]
> ./dock6[0x80b7b61]
> ./dock6[0x80661ae]
> /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xdc)[0xb7d42ebc]
> ./dock6(__gxx_personality_v0+0x14d)[0x804b651]
> ======= Memory map: ========
> 08048000-080f9000 r-xp 00000000 08:11 3671101    /home/andre/dock6/bin/dock6
> 080f9000-080fa000 rw-p 000b0000 08:11 3671101    /home/andre/dock6/bin/dock6
> 080fa000-082e2000 rw-p 080fa000 00:00 0          [heap]
> b45ad000-b46ae000 rw-p b45ad000 00:00 0
> b6100000-b6121000 rw-p b6100000 00:00 0
> b6121000-b6200000 ---p b6121000 00:00 0
> b62f9000-b7d2d000 rw-p b62f9000 00:00 0
> b7d2d000-b7e68000 r-xp 00000000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e68000-b7e69000 r--p 0013b000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e69000-b7e6b000 rw-p 0013c000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e6b000-b7e6e000 rw-p b7e6b000 00:00 0
> b7e6e000-b7e79000 r-xp 00000000 08:11 1933376    /lib/libgcc_s.so.1
> b7e79000-b7e7a000 rw-p 0000a000 08:11 1933376    /lib/libgcc_s.so.1
> b7e7a000-b7e9f000 r-xp 00000000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> b7e9f000-b7ea1000 rw-p 00024000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> b7ea1000-b7ea2000 rw-p b7ea1000 00:00 0
> b7ea2000-b7f81000 r-xp 00000000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f81000-b7f84000 r--p 000de000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f84000-b7f86000 rw-p 000e1000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f86000-b7f8c000 rw-p b7f86000 00:00 0
> b7f8c000-b7f9f000 r-xp 00000000 08:11 1936638
> /lib/tls/i686/cmov/libpthread-2.5.so
> b7f9f000-b7fa1000 rw-p 00013000 08:11 1936638
> /lib/tls/i686/cmov/libpthread-2.5.so
> b7fa1000-b7fa3000 rw-p b7fa1000 00:00 0
> b7fae000-b7fb1000 rw-p b7fae000 00:00 0
> b7fb1000-b7fca000 r-xp 00000000 08:11 1933333    /lib/ld-2.5.so
> b7fca000-b7fcc000 rw-p 00019000 08:11 1933333    /lib/ld-2.5.so
> bf8f2000-bf907000 rw-p bf8f2000 00:00 0          [stack]
> ffffe000-fffff000 r-xp 00000000 00:00 0          [vdso]
> Aborted (core dumped)
> andre at andre-desktop:~/dock6/bin$ ./dock6 -i dock3_5_score.in >& dock.out
> *** glibc detected *** ./dock6: double free or corruption (!prev):
> 0x08182080 ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6[0xb7d4c7cd]
> /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7d4fe30]
> /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7f0ed11]
> /usr/lib/libstdc++.so.6(_ZdaPv+0x1d)[0xb7f0ed6d]
> ./dock6[0x805776f]
> ./dock6[0x80b7b61]
> ./dock6[0x80661ae]
> /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xdc)[0xb7cfaebc]
> ./dock6(__gxx_personality_v0+0x14d)[0x804b651]
> ======= Memory map: ========
> 08048000-080f9000 r-xp 00000000 08:11 3671101    /home/andre/dock6/bin/dock6
> 080f9000-080fa000 rw-p 000b0000 08:11 3671101    /home/andre/dock6/bin/dock6
> 080fa000-082e2000 rw-p 080fa000 00:00 0          [heap]
> b4565000-b4666000 rw-p b4565000 00:00 0
> b6100000-b6121000 rw-p b6100000 00:00 0
> b6121000-b6200000 ---p b6121000 00:00 0
> b62b1000-b7ce5000 rw-p b62b1000 00:00 0
> b7ce5000-b7e20000 r-xp 00000000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e20000-b7e21000 r--p 0013b000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e21000-b7e23000 rw-p 0013c000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> b7e23000-b7e26000 rw-p b7e23000 00:00 0
> b7e26000-b7e31000 r-xp 00000000 08:11 1933376    /lib/libgcc_s.so.1
> b7e31000-b7e32000 rw-p 0000a000 08:11 1933376    /lib/libgcc_s.so.1
> b7e32000-b7e57000 r-xp 00000000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> b7e57000-b7e59000 rw-p 00024000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> b7e59000-b7e5a000 rw-p b7e59000 00:00 0
> b7e5a000-b7f39000 r-xp 00000000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f39000-b7f3c000 r--p 000de000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f3c000-b7f3e000 rw-p 000e1000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> b7f3e000-b7f44000 rw-p b7f3e000 00:00 0
> b7f44000-b7f57000 r-xp 00000000 08:11 1936638
> /lib/tls/i686/cmov/libpthread-2.5.so
> b7f57000-b7f59000 rw-p 00013000 08:11 1936638
> /lib/tls/i686/cmov/libpthread-2.5.so
> b7f59000-b7f5b000 rw-p b7f59000 00:00 0
> b7f66000-b7f69000 rw-p b7f66000 00:00 0
> b7f69000-b7f82000 r-xp 00000000 08:11 1933333    /lib/ld-2.5.so
> b7f82000-b7f84000 rw-p 00019000 08:11 1933333    /lib/ld-2.5.so
> bfcce000-bfce3000 rw-p bfcce000 00:00 0          [stack]
> ffffe000-fffff000 r-xp 00000000 00:00 0          [vdso]
> Aborted (core dumped)
>
>
>
> I am using an Intel 6600 quad core with Ubuntu linux 7.04 (32bit
> version fully updated). Is it perhaps a CPU specific or Linux
> distribution specific problem?
>
> Attached is my INCHEM file for CHEMGRID generation, gconvert.in file
> to to convert the chemgrids and the dock.in file (dock3_5_score.in).
> The "sa0_solv.pdb" receptor used was created in Chimera using the "del
> HC" command. The rec+sph.crg file used to generate the electrostatics
> grid with Delphi was made by combining the selected_spheres.pdb and
> sa0_solv.pdb and saving it as rec+sph.pdb and then renaming it (is
> this correct).
>
> Thank you
> Kind regards
> Andre
>



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