Hi,
Since you're using an out-of-date development version of cpptraj this
is difficult to diagnose off-hand. I would say try reading the mol2
file in the fully up-to-date AT12 version of cpptraj. If it kicks back
the same error send me the mol2 file off-list and I'll see what's
going on.
-Dan
On Wed, Jan 16, 2013 at 4:04 PM, Shashidhar Rao <shashidharr.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jan 16 2013 - 16:30:02 PST
