[gmx-users] errors due to genbox

[wuxiao]

Dear GMXers,

   I try to generate gro file using genbox, but fail with some errors. Command lines are:

   genbox -ci B.gro -o Bb.gro -nmol 200 -box 3 3 3

   where B.gro is the coordinate file of vinyl alcohol residue.

   The errors are given as bellows. Please give me some hints to cope with these problem. Thanks a lot for any reply.

 

   Sincerely,

   Chaofu Wu

 

........

    success (now 1400 atoms)!*** glibc detected *** genbox: realloc(): invalid old size: 0x083e6a70 ***
======= Backtrace: =========
/lib/libc.so.6[0xb7db8cb1]
/lib/libc.so.6[0xb7dbb928]
/lib/libc.so.6(__libc_realloc+0x100)[0xb7dbca40]
genbox[0x815bd6c]
======= Memory map: ========
08048000-083d2000 r-xp 00000000 08:09 358678     /usr/local/gromacs/bin/genbox
083d2000-083d9000 rwxp 00389000 08:09 358678     /usr/local/gromacs/bin/genbox
083d9000-21bc3000 rwxp 083d9000 00:00 0          [heap]
b7c00000-b7c21000 rwxp b7c00000 00:00 0
b7c21000-b7d00000 ---p b7c21000 00:00 0
b7d50000-b7d51000 rwxp b7d50000 00:00 0
b7d51000-b7d53000 r-xp 00000000 08:09 17118      /lib/libdl-2.4.so
b7d53000-b7d55000 rwxp 00001000 08:09 17118      /lib/libdl-2.4.so
b7d55000-b7e70000 r-xp 00000000 08:09 17112      /lib/libc-2.4.so
b7e70000-b7e72000 r-xp 0011a000 08:09 17112      /lib/libc-2.4.so
b7e72000-b7e74000 rwxp 0011c000 08:09 17112      /lib/libc-2.4.so
b7e74000-b7e77000 rwxp b7e74000 00:00 0
b7e77000-b7f6b000 r-xp 00000000 08:09 33645      /usr/X11R6/lib/libX11.so.6.2
b7f6b000-b7f6e000 rwxp 000f4000 08:09 33645      /usr/X11R6/lib/libX11.so.6.2
b7f6e000-b7f6f000 rwxp b7f6e000 00:00 0
b7f6f000-b7f84000 r-xp 00000000 08:09 33639      /usr/X11R6/lib/libICE.so.6.4
b7f84000-b7f85000 rwxp 00014000 08:09 33639      /usr/X11R6/lib/libICE.so.6.4
b7f85000-b7f87000 rwxp b7f85000 00:00 0
b7f87000-b7f8f000 r-xp 00000000 08:09 33641      /usr/X11R6/lib/libSM.so.6.0
b7f8f000-b7f90000 rwxp 00007000 08:09 33641      /usr/X11R6/lib/libSM.so.6.0
b7f90000-b7fb3000 r-xp 00000000 08:09 17120      /lib/libm-2.4.so
b7fb3000-b7fb5000 rwxp 00022000 08:09 17120      /lib/libm-2.4.so
b7fb5000-b7fc6000 r-xp 00000000 08:09 17123      /lib/libnsl-2.4.so
b7fc6000-b7fc8000 rwxp 00010000 08:09 17123      /lib/libnsl-2.4.so
b7fc8000-b7fca000 rwxp b7fc8000 00:00 0
b7fd6000-b7fe2000 r-xp 00000000 08:09 331626     /usr/local/lib/libgcc_s.so.1
b7fe2000-b7fe3000 rwxp 0000c000 08:09 331626     /usr/local/lib/libgcc_s.so.1
b7fe3000-b7fe5000 rwxp b7fe3000 00:00 0
b7fe5000-b7fff000 r-xp 00000000 08:09 17105      /lib/ld-2.4.so
b7fff000-b8001000 rwxp 0001a000 08:09 17105      /lib/ld-2.4.so
bffb3000-bffca000 rwxp bffb3000 00:00 0          [stack]
ffffe000-fffff000 ---p 00000000 00:00 0          [vdso]
Aborted


_________________________________________________________________
心跳斗地主新版体验，给你360度的心跳体验！
http://club.msn.cn/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090921/3bc77b7e/attachment.html>