Hi,
The tokenize() routine is part of ptraj's mask parser, so something is
going wrong there. I presume that the ptraj output is among the
intermediate files written out, so that could be a good place to start.
My recommendation however is to upgrade to AmberTools 14 as it contains
many improvements over the previous versions.
-Dan
On Tuesday, April 22, 2014, Kipp Johnson <kippjohnson.uchicago.edu> wrote:
> I would be grateful if someone could point out the cause for this error
> message I receive when I attempt to obtain quasiharmonic entropy using
> MMPBSA.py.MPI. The PB, GB, and nmode entropy calculations all appear to
> work correctly when I performed them earlier.
>
> #### MMPBSA.py.MPY infile ######
> &general
> startframe=1, endframe=180, interval=1,
> entropy=1,
> /
> &gb
> saltcon=0.1
> /
> &pb
> istrng=0.100
> /
>
>
> #### MMPBSA.py.MPI outfile ######
> Running MMPBSA.MPI on 16 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /software/amber-12-el6-x86_64/bin/mmpbsa_py_energy
> cpptraj found! Using /software/amber-12-el6-x86_64/bin/cpptraj
> ptraj found! Using /software/amber-12-el6-x86_64/bin/ptraj
> Preparing trajectories for simulation...
> 180 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with
> /software/amber-12-el6-x86_64/bin/mmpbsa_py_energy
> calculating complex contribution...
> Beginning PB calculations with
> /software/amber-12-el6-x86_64/bin/mmpbsa_py_energy
> calculating complex contribution...
> Beginning quasi-harmonic calculation...
>
>
> ERROR in tokenize(): wrong syntax
>
> CalcError: /software/amber-12-el6-x86_64/bin/ptraj failed with prmtop
> noMG_si_amber.prmtop!
> Error occured on rank 0.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> _______________________________________________
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> AMBER.ambermd.org <javascript:;>
> 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) 585-6208 (Fax)
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Received on Tue Apr 22 2014 - 17:30:02 PDT
