Hi amber users and developers,
I have a problem using ambmask.
ambmask -p com.TIP3PBOX.top -c com.TIP3PBOX.crd -find
'!:25,124,49,148>:4'
gives me the right group, but
com.TIP3PBOX.top
trajin prod.10ps_steps.mdcrd 1 5 1
strip :25,124,49,148>:4
trajout pocket.pdb
gives an error as follows:
...
PTRAJ: trajin prod.10ps_steps.mdcrd 1 5 1
Checking coordinates: prod.10ps_steps.mdcrd
PTRAJ: strip :25,124,49,148>:4
PTRAJ: trajout pocket.pdb
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 5 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (prod.10ps_steps.mdcrd) is an AMBER trajectory (with box info)
with 5 sets
OUTPUT COORDINATE FILE
File (pocket.pdb) is an AMBER trajectory (with box info)
ACTIONS
1> STRIP: 64 atoms will be removed from
trajectory: :1-5,:6.N, ... ,:10051.H2,:10052-10094
Processing AMBER trajectory file prod.10ps_steps.mdcrd
Set 1 .....
PTRAJ: Successfully read in 5 sets and processed 5 sets.
Dumping accumulated results (if any)
*** glibc detected *** ptraj: munmap_chunk(): invalid pointer:
0x000000000041fc43 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f359fe61928]
ptraj[0x4212d5]
ptraj[0x48c245]
ptraj[0x444ff9]
ptraj[0x44de2d]
ptraj[0x433c33]
ptraj[0x402a20]
/lib/libc.so.6(__libc_start_main+0xe6)[0x7f359fe0c1a6]
ptraj[0x402649]
======= Memory map: ========
00400000-0055e000 r-xp 00000000 08:03
11478768 /home/kuhn/amber10/bin/ptraj
0075d000-00767000 rw-p 0015d000 08:03
11478768 /home/kuhn/amber10/bin/ptraj
00767000-00771000 rw-p 00767000 00:00 0
022a9000-02537000 rw-p 022a9000 00:00 0
[heap]
7f359f589000-7f359f59f000 r-xp 00000000 08:03
22260186 /lib/libgcc_s.so.1
7f359f59f000-7f359f79f000 ---p 00016000 08:03
22260186 /lib/libgcc_s.so.1
7f359f79f000-7f359f7a0000 rw-p 00016000 08:03
22260186 /lib/libgcc_s.so.1
7f359f7b2000-7f359fdee000 rw-p 7f359f7b2000 00:00 0
7f359fdee000-7f359ff38000 r-xp 00000000 08:03
22260273 /lib/libc-2.7.so
7f359ff38000-7f35a0137000 ---p 0014a000 08:03
22260273 /lib/libc-2.7.so
7f35a0137000-7f35a013a000 r--p 00149000 08:03
22260273 /lib/libc-2.7.so
7f35a013a000-7f35a013c000 rw-p 0014c000 08:03
22260273 /lib/libc-2.7.so
7f35a013c000-7f35a0141000 rw-p 7f35a013c000 00:00 0
7f35a0141000-7f35a01c3000 r-xp 00000000 08:03
22260291 /lib/libm-2.7.so
7f35a01c3000-7f35a03c2000 ---p 00082000 08:03
22260291 /lib/libm-2.7.so
7f35a03c2000-7f35a03c4000 rw-p 00081000 08:03
22260291 /lib/libm-2.7.so
7f35a03c4000-7f35a03e0000 r-xp 00000000 08:03
22260265 /lib/ld-2.7.so
7f35a0410000-7f35a05ca000 rw-p 7f35a0410000 00:00 0
7f35a05db000-7f35a05df000 rw-p 7f35a05db000 00:00 0
7f35a05df000-7f35a05e1000 rw-p 0001b000 08:03
22260265 /lib/ld-2.7.so
7ffffb98a000-7ffffb99f000 rw-p 7ffffffea000 00:00 0
[stack]
7ffffb9ff000-7ffffba00000 r-xp 7ffffb9ff000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Abgebrochen
I'm using amber 10 and the 1.2 amber tools.
Thanks for any help.
Regards,
Oliver
--
Dipl.-Bioinf. Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Wed Jan 27 2010 - 02:00:03 PST
