Antechamber Task Details

CNT-26-40 Failed Antechamber

Task Info

Created Time

4/5/2023 7:05:39 AM

Updated Time

4/5/2023 7:05:49 AM

Progress

Output Files

Information

Output Message

Welcome to antechamber 20.0: molecular input file processor. Warning: Detected more than 10 Residue sequence numbers; this may be a large multiple residue PDB file; large multiple residue PDB files are not supported. This warning usually indicates a conceptual misunderstanding. We recommend reviewing the Information flow in Amber documentation and the antechamber tutorials. Continuing, but problems may be encountered. Info: The number of atoms (2560) exceeded MAXATOM. Warning: Detected more than 10 Residue sequence numbers; this may be a large multiple residue PDB file; large multiple residue PDB files are not supported. This warning usually indicates a conceptual misunderstanding. We recommend reviewing the Information flow in Amber documentation and the antechamber tutorials. Continuing, but problems may be encountered. Info: The bond number exceeds MAXBOND, reallocate memory automatically Info: The number of atoms (2560) exceeded MAXATOM.

Error Message

*** Error in `/usr/local/amber/bin/to_be_dispatched/bondtype': ======= Backtrace: ========= /lib64/libc.so.6(+0x7f754)[0x7fa14a4c6754] /lib64/libc.so.6(+0x8184b)[0x7fa14a4c884b] /lib64/libc.so.6(+0x83a48)[0x7fa14a4caa48] /lib64/libc.so.6(+0x86882)[0x7fa14a4cd882] /usr/local/amber/bin/to_be_dispatched/bondtype[0x41ffd /usr/local/amber/bin/to_be_dispatched/bondtype[0x41df5 /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fa14a46949 /usr/local/amber/bin/to_be_dispatched/bondtype[0x40105 ======= Memory map: ======== 00400000-00425000 r-xp 00000000 08:01 29367053 00624000-00625000 r--p 00024000 08:01 29367053 00625000-00626000 rw-p 00025000 08:01 29367053 00626000-0063e000 rw-p 00000000 00:00 0 00a8c000-00b24000 rw-p 00000000 00:00 0 7fa144000000-7fa144021000 rw-p 00000000 00:00 0 7fa144021000-7fa148000000 ---p 00000000 00:00 0 7fa14949f000-7fa1494b4000 r-xp 00000000 08:01 13514975 7fa1494b4000-7fa1496b3000 ---p 00015000 08:01 13514975 7fa1496b3000-7fa1496b4000 r--p 00014000 08:01 13514975 7fa1496b4000-7fa1496b5000 rw-p 00015000 08:01 13514975 7fa1496b5000-7fa1496b7000 r-xp 00000000 08:01 13501293 7fa1496b7000-7fa1498b6000 ---p 00002000 08:01 13501293 7fa1498b6000-7fa1498b7000 r--p 00001000 08:01 13501293 7fa1498b7000-7fa1498b8000 rw-p 00002000 08:01 13501293 7fa1498b8000-7fa1498bf000 r-xp 00000000 08:01 13501246 7fa1498bf000-7fa149abe000 ---p 00007000 08:01 13501246 7fa149abe000-7fa149abf000 r--p 00006000 08:01 13501246 7fa149abf000-7fa149ac0000 rw-p 00007000 08:01 13501246 7fa149ac0000-7fa149ac9000 r-xp 00000000 08:01 13504166 7fa149ac9000-7fa149cc8000 ---p 00009000 08:01 13504166 7fa149cc8000-7fa149cc9000 r--p 00008000 08:01 13504166 7fa149cc9000-7fa149cca000 rw-p 00009000 08:01 13504166 7fa149cca000-7fa149ccc000 r-xp 00000000 08:01 13501037 7fa149ccc000-7fa149ecc000 ---p 00002000 08:01 13501037 7fa149ecc000-7fa149ecd000 r--p 00002000 08:01 13501037 7fa149ecd000-7fa149ece000 rw-p 00003000 08:01 13501037 7fa149ece000-7fa149fb4000 r-xp 00000000 08:01 41557886 7fa149fb4000-7fa14a1b4000 ---p 000e6000 08:01 41557886 7fa14a1b4000-7fa14a1b8000 r--p 000e6000 08:01 41557886 7fa14a1b8000-7fa14a1be000 rw-p 000ea000 08:01 41557886 7fa14a1be000-7fa14a1c5000 rw-p 00000000 00:00 0 7fa14a1c5000-7fa14a241000 r-xp 00000000 08:01 41558103 7fa14a241000-7fa14a441000 ---p 0007c000 08:01 41558103 7fa14a441000-7fa14a442000 r--p 0007c000 08:01 41558103 7fa14a442000-7fa14a446000 rw-p 0007d000 08:01 41558103 7fa14a446000-7fa14a447000 rw-p 00000000 00:00 0 7fa14a447000-7fa14a609000 r-xp 00000000 08:01 13501016 7fa14a609000-7fa14a809000 ---p 001c2000 08:01 13501016 7fa14a809000-7fa14a80d000 r--p 001c2000 08:01 13501016 7fa14a80d000-7fa14a80f000 rw-p 001c6000 08:01 13501016 7fa14a80f000-7fa14a814000 rw-p 00000000 00:00 0 7fa14a814000-7fa14a82b000 r-xp 00000000 08:01 13501042 7fa14a82b000-7fa14aa2a000 ---p 00017000 08:01 13501042 7fa14aa2a000-7fa14aa2b000 r--p 00016000 08:01 13501042 7fa14aa2b000-7fa14aa2c000 rw-p 00017000 08:01 13501042 7fa14aa2c000-7fa14aa30000 rw-p 00000000 00:00 0 7fa14aa30000-7fa14aaf1000 r-xp 00000000 08:01 41558115 7fa14aaf1000-7fa14acf1000 ---p 000c1000 08:01 41558115 7fa14acf1000-7fa14acf2000 r--p 000c1000 08:01 41558115 7fa14acf2000-7fa14ad02000 rw-p 000c2000 08:01 41558115 7fa14ad02000-7fa14ad14000 rw-p 00000000 00:00 0 7fa14ad14000-7fa14ae15000 r-xp 00000000 08:01 13501047 7fa14ae15000-7fa14b014000 ---p 00101000 08:01 13501047 7fa14b014000-7fa14b015000 r--p 00100000 08:01 13501047 7fa14b015000-7fa14b016000 rw-p 00101000 08:01 13501047 7fa14b016000-7fa14b038000 r-xp 00000000 08:01 13501009 7fa14b14b000-7fa14b218000 rw-p 00000000 00:00 0 7fa14b234000-7fa14b237000 rw-p 00000000 00:00 0 7fa14b237000-7fa14b238000 r--p 00021000 08:01 13501009 7fa14b238000-7fa14b239000 rw-p 00022000 08:01 13501009 7fa14b239000-7fa14b23a000 rw-p 00000000 00:00 0 7fffe0752000-7fffe0773000 rw-p 00000000 00:00 0 7fffe07a6000-7fffe07a8000 r-xp 00000000 00:00 0 ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 /usr/local/amber/bin/bondtype: line 4: 11584 Aborted /usr/local/amber/bin/to_be_dispatched/antechamber: Cannot properly run "/usr/local/amber/bin/bondtype corrupted size vs. prev_size: 0x0000000000a8fe40 *** 3] d] 5] 9] /usr/local/amber/bin/to_be_dispatched/bondtype /usr/local/amber/bin/to_be_dispatched/bondtype /usr/local/amber/bin/to_be_dispatched/bondtype [heap] /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/libutil-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/librt-2.17.so /usr/lib64/libpciaccess.so.0.11.1 /usr/lib64/libpciaccess.so.0.11.1 /usr/lib64/libpciaccess.so.0.11.1 /usr/lib64/libpciaccess.so.0.11.1 /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /usr/lib64/libdl-2.17.so /opt/openmpi/lib/libopen-pal.so.20.10.1 /opt/openmpi/lib/libopen-pal.so.20.10.1 /opt/openmpi/lib/libopen-pal.so.20.10.1 /opt/openmpi/lib/libopen-pal.so.20.10.1 /opt/openmpi/lib/libopen-rte.so.20.10.1 /opt/openmpi/lib/libopen-rte.so.20.10.1 /opt/openmpi/lib/libopen-rte.so.20.10.1 /opt/openmpi/lib/libopen-rte.so.20.10.1 /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libc-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /usr/lib64/libpthread-2.17.so /opt/openmpi/lib/libmpi.so.20.10.1 /opt/openmpi/lib/libmpi.so.20.10.1 /opt/openmpi/lib/libmpi.so.20.10.1 /opt/openmpi/lib/libmpi.so.20.10.1 /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/libm-2.17.so /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so /usr/lib64/ld-2.17.so [stack] [vdso] [vsyscall] (core dumped) $AMBERHOME/bin/to_be_dispatched/bondtype "$@" Fatal Error! -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac".