Dear all,
I tried to convert my ligand pdb file to Mol2 file using antechamber.
But dont whats wrong but gave the following error and got aborted.
Can anyone with this
Running: /applications/smp/amber/10/
intelmpi-mkl/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC <
http://antechamber_bond_type.ac/> -f ac
Running: /applications/smp/amber/10/intelmpi-mkl/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC <
http://antechamber_ac.ac/> -p gaff
Total number of electrons: 79; net charge: 0
INFO: Number of electrons is odd: 79
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
Running: /applications/smp/amber/10/intelmpi-mkl/bin/mopac.sh
*** glibc detected *** /applications/smp/amber/10/intelmpi-mkl/bin/mopac:
malloc(): memory corruption: 0x60000000046fc1a0 ***
======= Backtrace: =========
/lib/libc.so.6.1[0x20000000004af090]
/lib/libc.so.6.1[0x20000000004b4870]
/lib/libc.so.6.1(malloc+0x4709f8)[0x20000000004b7800]
/lib/libc.so.6.1(catopen+0x3e9278)[0x2000000000430ab0]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x400000000018a990]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x4000000000189810]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x400000000018da50]
[0xa0000000000107e0]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x4000000000112850]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x400000000005b850]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x40000000000686e0]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x40000000000661f0]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x4000000000044510]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x40000000000b5870]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x40000000000141f0]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x4000000000003350]
/lib/libc.so.6.1(__libc_start_main+0x3c0508)[0x2000000000407d60]
/applications/smp/amber/10/intelmpi-mkl/bin/mopac[0x4000000000003180]
======= Memory map: ========
00000000-00004000 r--p 00000000 00:00 0
2000000000000000-2000000000038000 r-xp 00000000 08:02 13345033
/lib/ld-2.4.so
2000000000038000-200000000003c000 rw-p 2000000000038000 00:00 0
2000000000044000-200000000004c000 rw-p 00034000 08:02 13345033
/lib/ld-2.4.so
2000000000064000-20000000002c8000 rwxp 00000000 08:02 145594478
/usr/lib/sgi/intel9/libimf.so.6
20000000002c8000-20000000002d4000 ---p 00264000 08:02 145594478
/usr/lib/sgi/intel9/libimf.so.6
20000000002d4000-2000000000314000 rw-p 00260000 08:02 145594478
/usr/lib/sgi/intel9/libimf.so.6
2000000000314000-20000000003d0000 r-xp 00000000 08:02 13345048
/lib/libm-2.4.so
20000000003d0000-20000000003dc000 ---p 000bc000 08:02 13345048
/lib/libm-2.4.so
20000000003dc000-20000000003e4000 rw-p 000b8000 08:02 13345048
/lib/libm-2.4.so
20000000003e4000-2000000000620000 r-xp 00000000 08:02 13345040
/lib/libc-2.4.so
2000000000620000-200000000062c000 ---p 0023c000 08:02 13345040
/lib/libc-2.4.so
200000000062c000-2000000000634000 rw-p 00238000 08:02 13345040
/lib/libc-2.4.so
2000000000634000-2000000000638000 rw-p 2000000000634000 00:00 0
2000000000638000-200000000065c000 r-xp 00000000 00:15 1611452902
/applications/smp/gcc/4.4/lib/libgcc_s.so.1
200000000065c000-2000000000668000 ---p 00024000 00:15 1611452902
/applications/smp/gcc/4.4/lib/libgcc_s.so.1
2000000000668000-200000000066c000 rw-p 00020000 00:15 1611452902
/applications/smp/gcc/4.4/lib/libgcc_s.so.1
200000000066c000-2000000000674000 r-xp 00000000 08:02 13345046
/lib/libdl-2.4.so
2000000000674000-2000000000680000 ---p 00008000 08:02 13345046
/lib/libdl-2.4.so
2000000000680000-2000000000684000 rw-p 00004000 08:02 13345046
/lib/libdl-2.4.so
2000000000684000-2000000000694000 r-xp 00000000 00:15 1611452905
/applications/smp/gcc/4.4/lib/libunwind.so.7
2000000000694000-20000000006a0000 ---p 00010000 00:15 1611452905
/applications/smp/gcc/4.4/lib/libunwind.so.7
20000000006a0000-20000000006a4000 rw-p 0000c000 00:15 1611452905
/applications/smp/gcc/4.4/lib/libunwind.so.7
20000000006a4000-20000000006d0000 rw-p 20000000006a4000 00:00 0
2000000000700000-2000000000724000 rw-p 2000000000700000 00:00 0
2000000000724000-2000000000800000 ---p 2000000000724000 00:00 0
4000000000000000-40000000002c4000 r-xp 00000000 00:15 1073838591
/applications/smp/amber/10/intelmpi-mkl/bin/mopac
6000000000000000-6000000000070000 rw-p 002c0000 00:15 1073838591
/applications/smp/amber/10/intelmpi-mkl/bin/mopac
6000000000070000-6000000004720000 rw-p 6000000000070000 00:00 0
[heap]
603fffffffffc000-6040000000000000 rw-p 603fffffffffc000 00:00 0
607fffffff2dc000-607fffffff330000 rwxp 607fffffff2dc000 00:00 0
[stack]
a000000000000000-a000000000020000 ---p 00000000 00:00 0
[vdso]
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
. A000000000010621 Unknown Unknown Unknown
libc.so.6.1 20000000004342E0 Unknown Unknown Unknown
libc.so.6.1 2000000000436930 Unknown Unknown Unknown
libc.so.6.1 20000000004A2540 Unknown Unknown Unknown
libc.so.6.1 20000000004AF090 Unknown Unknown Unknown
libc.so.6.1 20000000004B4870 Unknown Unknown Unknown
libc.so.6.1 20000000004B7800 Unknown Unknown Unknown
libc.so.6.1 2000000000430AB0 Unknown Unknown Unknown
mopac 400000000018A990 Unknown Unknown Unknown
mopac 4000000000189810 Unknown Unknown Unknown
mopac 400000000018DA50 Unknown Unknown Unknown
. A0000000000107E0 Unknown Unknown Unknown
mopac 4000000000112850 Unknown Unknown Unknown
mopac 400000000005B850 Unknown Unknown Unknown
mopac 40000000000686E0 Unknown Unknown Unknown
mopac 40000000000661F0 Unknown Unknown Unknown
mopac 4000000000044510 Unknown Unknown Unknown
mopac 40000000000B5870 Unknown Unknown Unknown
mopac 40000000000141F0 Unknown Unknown Unknown
mopac 4000000000003350 Unknown Unknown Unknown
libc.so.6.1 2000000000407D60 Unknown Unknown Unknown
mopac 4000000000003180 Unknown Unknown Unknown
Thank you,
Anogna
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Received on Wed Sep 12 2012 - 01:30:03 PDT
