I obtained the following errors when I attempted to read a MOL2 file in the
command "parm". The MOL2 file was generated in the Schrodinger's maestro
interface and was readable without any errors in Sybyl-X from Tripos.
Can anyone please suggest a possible path forward?
thanks,
Shashi Rao
===============
shashi.truffle:/u2/shashi_local/P38/DESMOND_MD_JUN27$ cpptraj
CPPTRAJ: Trajectory Analysis. V13.8b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> parm 3LFE_lig_complex_Jan16.mol2
[parm 3LFE_lig_complex_Jan16.mol2]
Reading Mol2 file 3LFE_lig_complex_Jan16.mol2 as topology file.
Mol2 contains 5484 atoms, 354 residues,
3LFE_lig_complex_Jan16.mol2: determining molecule info from bonds.
*** glibc detected *** cpptraj: free(): invalid next size (fast):
0x000000000214f0b0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7ff3ec698b96]
cpptraj[0x426d27]
cpptraj[0x481ef4]
cpptraj[0x4d08f2]
cpptraj[0x4c28c7]
cpptraj[0x4c377c]
cpptraj[0x4c3e34]
cpptraj[0x4907f7]
cpptraj[0x4099c4]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7ff3ec63b76d]
cpptraj[0x409c21]
======= Memory map: ========
00400000-005ca000 r-xp 00000000 00:30 2150603013
/net/casegroup2/u2/shashi/amber12/bin/cpptraj
007c9000-007ca000 r--p 001c9000 00:30 2150603013
/net/casegroup2/u2/shashi/amber12/bin/cpptraj
007ca000-007cb000 rw-p 001ca000 00:30 2150603013
/net/casegroup2/u2/shashi/amber12/bin/cpptraj
007cb000-007de000 rw-p 00000000 00:00 0
0214a000-021eb000 rw-p 00000000 00:00 0
[heap]
7ff3ec2d3000-7ff3ec3e4000 rw-p 00000000 00:00 0
7ff3ec3e4000-7ff3ec419000 r-xp 00000000 08:02 2747311
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7ff3ec419000-7ff3ec618000 ---p 00035000 08:02 2747311
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7ff3ec618000-7ff3ec619000 r--p 00034000 08:02 2747311
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7ff3ec619000-7ff3ec61a000 rw-p 00035000 08:02 2747311
/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7ff3ec61a000-7ff3ec7cf000 r-xp 00000000 08:02 393356
/lib/x86_64-linux-gnu/libc-2.15.so
7ff3ec7cf000-7ff3ec9ce000 ---p 001b5000 08:02 393356
/lib/x86_64-linux-gnu/libc-2.15.so
7ff3ec9ce000-7ff3ec9d2000 r--p 001b4000 08:02 393356
/lib/x86_64-linux-gnu/libc-2.15.so
7ff3ec9d2000-7ff3ec9d4000 rw-p 001b8000 08:02 393356
/lib/x86_64-linux-gnu/libc-2.15.so
7ff3ec9d4000-7ff3ec9d9000 rw-p 00000000 00:00 0
7ff3ec9d9000-7ff3ec9ee000 r-xp 00000000 08:02 392481
/lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ec9ee000-7ff3ecbed000 ---p 00015000 08:02 392481
/lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ecbed000-7ff3ecbee000 r--p 00014000 08:02 392481
/lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ecbee000-7ff3ecbef000 rw-p 00015000 08:02 392481
/lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ecbef000-7ff3eccea000 r-xp 00000000 08:02 393391
/lib/x86_64-linux-gnu/libm-2.15.so
7ff3eccea000-7ff3ecee9000 ---p 000fb000 08:02 393391
/lib/x86_64-linux-gnu/libm-2.15.so
7ff3ecee9000-7ff3eceea000 r--p 000fa000 08:02 393391
/lib/x86_64-linux-gnu/libm-2.15.so
7ff3eceea000-7ff3eceeb000 rw-p 000fb000 08:02 393391
/lib/x86_64-linux-gnu/libm-2.15.so
7ff3eceeb000-7ff3ecfcd000 r-xp 00000000 08:02 2751588
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff3ecfcd000-7ff3ed1cc000 ---p 000e2000 08:02 2751588
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff3ed1cc000-7ff3ed1d4000 r--p 000e1000 08:02 2751588
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff3ed1d4000-7ff3ed1d6000 rw-p 000e9000 08:02 2751588
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7ff3ed1d6000-7ff3ed1eb000 rw-p 00000000 00:00 0
7ff3ed1eb000-7ff3ed2ff000 r-xp 00000000 08:02 2754034
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7ff3ed2ff000-7ff3ed4ff000 ---p 00114000 08:02 2754034
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7ff3ed4ff000-7ff3ed500000 r--p 00114000 08:02 2754034
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7ff3ed500000-7ff3ed502000 rw-p 00115000 08:02 2754034
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7ff3ed502000-7ff3ed511000 r-xp 00000000 08:02 396456
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7ff3ed511000-7ff3ed710000 ---p 0000f000 08:02 396456
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7ff3ed710000-7ff3ed711000 r--p 0000e000 08:02 396456
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7ff3ed711000-7ff3ed712000 rw-p 0000f000 08:02 396456
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7ff3ed712000-7ff3ed728000 r-xp 00000000 08:02 397546
/lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff3ed728000-7ff3ed927000 ---p 00016000 08:02 397546
/lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff3ed927000-7ff3ed928000 r--p 00015000 08:02 397546
/lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff3ed928000-7ff3ed929000 rw-p 00016000 08:02 397546
/lib/x86_64-linux-gnu/libz.so.1.2.3.4
7ff3ed929000-7ff3ed94b000 r-xp 00000000 08:02 396304
/lib/x86_64-linux-gnu/ld-2.15.so
7ff3edb23000-7ff3edb2a000 rw-p 00000000 00:00 0
7ff3edb46000-7ff3edb4b000 rw-p 00000000 00:00 0
7ff3edb4b000-7ff3edb4c000 r--p 00022000 08:02 396304
/lib/x86_64-linux-gnu/ld-2.15.so
7ff3edb4c000-7ff3edb4e000 rw-p 00023000 08:02 396304
/lib/x86_64-linux-gnu/ld-2.15.so
7fff2fb1b000-7fff2fb3d000 rw-p 00000000 00:00 0
[stack]
7fff2fbff000-7fff2fc00000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted (core dumped)
======================================================
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Wed Jan 16 2013 - 15:30:03 PST
