Hi Dan,
I have this psf file which I converted from LAMMPS and topotools. I know
its a round about way of doing things. I am trying to read the psf file in
ptraj. It seems fine but then when I try to do covariance matrix
calculations,it gives me a segmentation fault. I tried the other commands
and it seems to work such as distance etc.
However I tried used cpptraj and it doesnot seem to read the psf file at
all:
Any help will be greatly appreciated.
thanks,
ganesh
./cpptraj nm.psf
CPPTRAJ: Trajectory Analysis. V12.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Reading Charmm PSF file nm.psf as topology file.
PSF: !NATOM tag found, natom=13440
0 bonds to hydrogen.
11520 bonds to non-hydrogen.
PSF contains 13440 atoms, 7680 residues, 0 molecules.
*** stack smashing detected ***: ./cpptraj terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fc47c34d167]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x7fc47c34d130]
./cpptraj[0x4ef8f8]
./cpptraj[0x4e99df]
./cpptraj[0x424bc5]
./cpptraj[0x424a2e]
./cpptraj[0x40412f]
./cpptraj[0x404255]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7fc47c26aeff]
./cpptraj[0x4039c9]
======= Memory map: ========
00400000-0053c000 r-xp 00000000 08:07 23618541
/home/ganesh/cpptraj
0073b000-0073c000 r--p 0013b000 08:07 23618541
/home/ganesh/cpptraj
0073c000-0073d000 rw-p 0013c000 08:07 23618541
/home/ganesh/cpptraj
00840000-008f1000 rw-p 00000000 00:00 0
[heap]
7fc47c24c000-7fc47c3d9000 r-xp 00000000 08:06 5572
/lib/x86_64-linux-gnu/libc-2.13.so
7fc47c3d9000-7fc47c5d9000 ---p 0018d000 08:06 5572
/lib/x86_64-linux-gnu/libc-2.13.so
7fc47c5d9000-7fc47c5dd000 r--p 0018d000 08:06 5572
/lib/x86_64-linux-gnu/libc-2.13.so
7fc47c5dd000-7fc47c5de000 rw-p 00191000 08:06 5572
/lib/x86_64-linux-gnu/libc-2.13.so
7fc47c5de000-7fc47c5e4000 rw-p 00000000 00:00 0
7fc47c5e4000-7fc47c5f9000 r-xp 00000000 08:06 5127
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fc47c5f9000-7fc47c7f8000 ---p 00015000 08:06 5127
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fc47c7f8000-7fc47c7f9000 r--p 00014000 08:06 5127
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fc47c7f9000-7fc47c7fa000 rw-p 00015000 08:06 5127
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fc47c7fa000-7fc47c87e000 r-xp 00000000 08:06 6667
/lib/x86_64-linux-gnu/libm-2.13.so
7fc47c87e000-7fc47ca7d000 ---p 00084000 08:06 6667
/lib/x86_64-linux-gnu/libm-2.13.so
7fc47ca7d000-7fc47ca7e000 r--p 00083000 08:06 6667
/lib/x86_64-linux-gnu/libm-2.13.so
7fc47ca7e000-7fc47ca7f000 rw-p 00084000 08:06 6667
/lib/x86_64-linux-gnu/libm-2.13.so
7fc47ca7f000-7fc47cb67000 r-xp 00000000 08:06 143099
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fc47cb67000-7fc47cd66000 ---p 000e8000 08:06 143099
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fc47cd66000-7fc47cd6e000 r--p 000e7000 08:06 143099
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fc47cd6e000-7fc47cd70000 rw-p 000ef000 08:06 143099
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fc47cd70000-7fc47cd85000 rw-p 00000000 00:00 0
7fc47cd85000-7fc47ce66000 r-xp 00000000 08:06 142935
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fc47ce66000-7fc47d066000 ---p 000e1000 08:06 142935
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fc47d066000-7fc47d067000 r--p 000e1000 08:06 142935
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fc47d067000-7fc47d068000 rw-p 000e2000 08:06 142935
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fc47d068000-7fc47d069000 rw-p 00000000 00:00 0
7fc47d069000-7fc47d08a000 r-xp 00000000 08:06 6669
/lib/x86_64-linux-gnu/ld-2.13.so
7fc47d25f000-7fc47d264000 rw-p 00000000 00:00 0
7fc47d285000-7fc47d289000 rw-p 00000000 00:00 0
7fc47d289000-7fc47d28a000 r--p 00020000 08:06 6669
/lib/x86_64-linux-gnu/ld-2.13.so
7fc47d28a000-7fc47d28c000 rw-p 00021000 08:06 6669
/lib/x86_64-linux-gnu/ld-2.13.so
7fff13afe000-7fff13b1f000 rw-p 00000000 00:00 0
[stack]
7fff13bb9000-7fff13bba000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted
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Received on Fri Mar 29 2013 - 12:00:02 PDT
