Hello,
This advice is unrelated to the problem you're having, but is still
something worth pointing out.
On Wed, Jan 27, 2010 at 4:36 AM, Oliver Kuhn <oak.amber.web.de> wrote:
> 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
This will write an amber mdcrd file named "pocket.pdb" rather than 5
PDB files. If you want to write 5 PDB files, change the trajout line
to:
trajout pocket.pdb pdb
to tell it to write out PDBs. This will write pocket.pdb.1
pocket.pdb.2 ... etc.
>
> 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)
No idea why this is happening. Perhaps a debugger (if compiled with
the -g option for gnu compilers and optimization level 0) will point
out the offending line.
>
> *** 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.
ptraj included with AmberTools 1.3 is much much faster, and the
upgrade is typically a good idea.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 27 2010 - 06:00:09 PST
