[gmx-users] topolbuild error

Thu Feb 19 17:40:17 CET 2015

Dear Ray
I tried to use another .mol2 file. I use USCF chimera to save it.

@<TRIPOS>MOLECULE
OXL.pdb
6 5 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1 C1         47.7640   52.0960   49.3000 C.2       1 OXL    0.0000
      2 C2         48.9620   53.0060   49.8530 C.2       1 OXL    0.0000
      3 O1         47.5730   51.0150   49.8280 O.co2     1 OXL    0.0000
      4 O2         49.5800   52.4680   50.7770 O.co2     1 OXL    0.0000
      5 O3         47.0570   52.5150   48.3410 O.co2     1 OXL    0.0000
      6 O4         49.0630   54.1080   49.2490 O.co2     1 OXL    0.0000
@<TRIPOS>BOND
     1    1    2 2
     2    1    3 2
     3    1    5 2
     4    2    4 2
     5    2    6 2
@<TRIPOS>SUBSTRUCTURE
     1 OXL     1 RESIDUE           4 A     OXL     0 ROOT

Unfortunately, I confronted the new error:

Fatal error.
Source code file: readmol2.c, line: 419
File read to end without finding molecule record reading mol2 file.
I am looking forward to getting your guidance.

On Thu, Feb 19, 2015 at 7:06 PM, Ray, Bruce D <bray at iupui.edu> wrote:

>
> On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, <zahraghanbari10 at gmail.com>
> wrote:
>
> > hi
> > I installed topolbuild version 1.3. I used following command line:
> > ./topolbuild -dir /home/supermicro/topolbuild1_3/dat/gromacs -ff oplsaa
> -n
> > OXL -r OXL -meas -rename -move
> > I encountered with following error:
> > *** Error in `./topolbuild': free(): invalid next size (fast):
> > 0x0000000001b752a0 ***
> > ======= Backtrace: =========
> > /lib/x86_64-linux-gnu/libc.so.6(+0x80996)[0x7f9fa8024996]
> > ./topolbuild[0x40701c]
> > ./topolbuild[0x40b01e]
> > ./topolbuild[0x403226]
> > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f9fa7fc5de5]
> > ./topolbuild[0x401059]
> > ======= Memory map: ========
> > 00400000-0042c000 r-xp 00000000 08:01 25430000
> > /home/supermicro/topolbuild1_3/src/topolbuild
> > 0062b000-0062c000 r--p 0002b000 08:01 25430000
> > /home/supermicro/topolbuild1_3/src/topolbuild
> > 0062c000-0062d000 rw-p 0002c000 08:01 25430000
> > /home/supermicro/topolbuild1_3/src/topolbuild
> > 0062d000-0062e000 rw-p 00000000 00:00 0
> > 01b74000-01b95000 rw-p 00000000 00:00 0
> > [heap]
> > 7f9fa7d8e000-7f9fa7da3000 r-xp 00000000 08:01 58458205
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f9fa7da3000-7f9fa7fa2000 ---p 00015000 08:01 58458205
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f9fa7fa2000-7f9fa7fa3000 r--p 00014000 08:01 58458205
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f9fa7fa3000-7f9fa7fa4000 rw-p 00015000 08:01 58458205
> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> > 7f9fa7fa4000-7f9fa8161000 r-xp 00000000 08:01 58461967
> > /lib/x86_64-linux-gnu/libc-2.17.so
> > 7f9fa8161000-7f9fa8361000 ---p 001bd000 08:01 58461967
> > /lib/x86_64-linux-gnu/libc-2.17.so
> > 7f9fa8361000-7f9fa8365000 r--p 001bd000 08:01 58461967
> > /lib/x86_64-linux-gnu/libc-2.17.so
> > 7f9fa8365000-7f9fa8367000 rw-p 001c1000 08:01 58461967
> > /lib/x86_64-linux-gnu/libc-2.17.so
> > 7f9fa8367000-7f9fa836c000 rw-p 00000000 00:00 0
> > 7f9fa836c000-7f9fa846f000 r-xp 00000000 08:01 58462018
> > /lib/x86_64-linux-gnu/libm-2.17.so
> > 7f9fa846f000-7f9fa866e000 ---p 00103000 08:01 58462018
> > /lib/x86_64-linux-gnu/libm-2.17.so
> > 7f9fa866e000-7f9fa866f000 r--p 00102000 08:01 58462018
> > /lib/x86_64-linux-gnu/libm-2.17.so
> > 7f9fa866f000-7f9fa8670000 rw-p 00103000 08:01 58462018
> > /lib/x86_64-linux-gnu/libm-2.17.so
> > 7f9fa8670000-7f9fa8693000 r-xp 00000000 08:01 58461943
> > /lib/x86_64-linux-gnu/ld-2.17.so
> > 7f9fa8874000-7f9fa8877000 rw-p 00000000 00:00 0
> > 7f9fa888e000-7f9fa8892000 rw-p 00000000 00:00 0
> > 7f9fa8892000-7f9fa8893000 r--p 00022000 08:01 58461943
> > /lib/x86_64-linux-gnu/ld-2.17.so
> > 7f9fa8893000-7f9fa8895000 rw-p 00023000 08:01 58461943
> > /lib/x86_64-linux-gnu/ld-2.17.so
> > 7fffd7450000-7fffd7471000 rw-p 00000000 00:00 0
> > [stack]
> > 7fffd749a000-7fffd749c000 r-xp 00000000 00:00 0
> > [vdso]
> > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> > [vsyscall]
> > Aborted (core dumped)
> > how to resolve this problem?
> > any help will highly appreciated.
> >
>
> This looks like a compilation problem.  The error message is not a
> topolbuild
> error.  From what is shown, I cannot tell from where the call to free()
> was made
> and cannot give further help until that can be determined.
>
>
> --
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St., Rm. LD-061
> Indianapolis, IN  46202
>
>
>
> --
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St., Rm. LD-061
> Indianapolis, IN  46202
>
>
> --
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