[Dock-fans] Sphere Selector Error

Trent E. Balius tbalius at aol.com
Wed Jun 22 11:28:53 PDT 2011


How many spheres are in the rec.sph file?  

Try setting stack size to unlimited:

For example in csh:

limit stacksize unlimit

If this does not work send me your sphere and mol2 files.


 I hope this helps,


Trent 

 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Wed, Jun 22, 2011 2:07 pm
Subject: Re: Sphere Selector Error




Hi, Trent:

The command I run is shown below:
../../../bin/sphere_selector rec.sph ../1_struct/lig_charged.mol2 10.0

I tried the sample script it works but if I run with my own protein, I kept receiving stack smashing error. The ligand I tried to dock is an ATP molecule.

Please feel free to let me know if you need any additional information.

Thank you,
Ben

--- On Wed, 6/22/11, Trent E. Balius <tbalius at aol.com> wrote:


From: Trent E. Balius <tbalius at aol.com>
Subject: Re: Sphere Selector Error
To: benny_yc_lo at yahoo.com, dock-fans at mailman.docking.org
Date: Wednesday, June 22, 2011, 6:33 AM


 Hi Ben,

I need more information.  Could you provide the command you are running and more details? 

Trent


 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: tbalius at ams.sunysb.edu
Sent: Tue, Jun 21, 2011 6:41 pm
Subject: Sphere Selector Error




Hi, Trent:

I try to use the sphere selector but receive the following error:

*** stack smashing detected ***: ../../../bin/sphere_selector terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x50)[0x2e0970]
/lib/libc.so.6(+0xe591a)[0x2e091a]
../../../bin/sphere_selector[0x804941a]
../../../bin/sphere_selector[0x8049511]
/lib/libc.so.6(__libc_start_main+0xe7)[0x211ce7]
../../../bin/sphere_selector[0x8048b71]
======= Memory map: ========
00110000-001ef000 r-xp 00000000 08:05 11275861   /usr/lib/libstdc++.so.6.0.14
001ef000-001f3000 r--p 000de000 08:05 11275861   /usr/lib/libstdc++.so.6.0.14
001f3000-001f4000 rw-p 000e2000 08:05 11275861   /usr/lib/libstdc++.so.6.0.14
001f4000-001fb000 rw-p 00000000 00:00 0 
001fb000-00352000 r-xp 00000000 08:05 1573626    /lib/libc-2.12.1.so
00352000-00354000 r--p 00157000 08:05 1573626    /lib/libc-2.12.1.so
00354000-00355000 rw-p 00159000 08:05 1573626    /lib/libc-2.12.1.so
00355000-00358000 rw-p 00000000 00:00 0 
00409000-00423000 r-xp 00000000 08:05 1572943    /lib/libgcc_s.so.1
00423000-00424000 r--p 00019000 08:05 1572943    /lib/libgcc_s.so.1
00424000-00425000 rw-p 0001a000 08:05 1572943    /lib/libgcc_s.so.1
0086e000-0086f000 r-xp 00000000 00:00 0          [vdso]
008ef000-0090b000 r-xp 00000000 08:05 1573623    /lib/ld-2.12.1.so
0090b000-0090c000 r--p 0001b000 08:05 1573623    /lib/ld-2.12.1.so
0090c000-0090d000 rw-p 0001c000 08:05 1573623    /lib/ld-2.12.1.so
00f65000-00f89000 r-xp 00000000 08:05 1573630    /lib/libm-2.12.1.so
00f89000-00f8a000 r--p 00023000 08:05 1573630    /lib/libm-2.12.1.so
00f8a000-00f8b000 rw-p 00024000 08:05 1573630    /lib/libm-2.12.1.so
08048000-0804a000 r-xp 00000000 08:05 5380267    /home/ben/Desktop/dock6/bin/sphere_selector
0804a000-0804b000 r--p 00001000 08:05 5380267    /home/ben/Desktop/dock6/bin/sphere_selector
0804b000-0804c000 rw-p 00002000 08:05 5380267    /home/ben/Desktop/dock6/bin/sphere_selector
08167000-08188000 rw-p 00000000 00:00 0          [heap]
b7681000-b770d000 rw-p 00000000 00:00 0 
b771e000-b7721000 rw-p 00000000 00:00 0 
bf831000-bf852000 rw-p 00000000 00:00 0          [stack]
Aborted

Please help,

Thank you,
Ben



 



 
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