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 <b...@iupui.edu> wrote:
>
> On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, <zahraghanbar...@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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