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

BA S bas007ster at gmail.com
Wed Sep 12 11:30:12 PDT 2007


Hi all

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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