On Wed, Jan 23, 2013 at 10:56 AM, Jagur Lambix <jagurlambix.gmail.com>wrote:
> Hi Dan,
> Thanks for your reply.
> I would install the upgraded ptraj from AmberTools 12.
>
> I was using the ptraj and part of the input file is described below:
> trajin /home/usr/prod_1ns.mdcrd.gz
> trajin /home/usr/prod_2ns.mdcrd.gz
> trajin /home/usr/prod_3ns.mdcrd.gz
> trajin /home/usr/prod_4ns.mdcrd.gz
> trajin /home/usr/prod_5ns.mdcrd.gz
> strip :WAT
> strip :Cl-
> center :1-200
> image center familiar
> rms first out rmsd-5ns :1-200.CA
> atomicfluct out rmsf-5ns byres
>
>
You can combine the strip commands into one command:
strip :WAT,Cl-
You can also use the autoimage command in cpptraj more easily:
trajin blah
trajin blah2
...
autoimage
strip :WAT,Cl-
rms first out rmsd-5ns :1-200.CA
atomicfluct out rmsf-5ns byres
One other comment -- I have almost always seen atomic fluctuations
calculated with respect to an average structure, so the RMS fit would be
done with respect to a reference (which is a previously calculated average
structure).
> However, in the mean time I am providing the entire error message came
> while running ptraj as follows:
>
> *** glibc detected *** /usr/apps/amber11/exe/ptraj: munmap_chunk(): invalid
> pointer: 0x000000001faebfd0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6(cfree+0x1b6)[0x3008672b96]
> /usr/apps/amber11/exe/ptraj[0x42194e]
> /usr/apps/amber11/exe/ptraj[0x422a54]
> /usr/apps/amber11/exe/ptraj[0x422b16]
> /usr/apps/amber11/exe/ptraj[0x42a896]
> /usr/apps/amber11/exe/ptraj[0x44a342]
> /usr/apps/amber11/exe/ptraj[0x450c84]
> /usr/apps/amber11/exe/ptraj[0x451c40]
> /usr/apps/amber11/exe/ptraj[0x437d27]
> /usr/apps/amber11/exe/ptraj[0x40272a]
> [snip]
> [stack]
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
> [vdso]
>
> I hope, this error message may provide the clue to trace the fault.
>
It will provide almost no help. This back trace is effectively useless
(maybe it tells you how many functions deep the error occurred in). This
would either need to be re-run on a system with debug symbols added and
that back trace reported or some developer would need to be able to
reproduce the error to properly address the bug.
If it works in AmberTools 12, either ptraj or cpptraj, the likelihood of
someone spending time to fix an already-fixed bug is pretty low (unless the
fix is trivial).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 23 2013 - 10:30:03 PST
