It seems that there is some problem with writing intermediate trajectories,
as error message suggests
Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 2
Error: Box line=[ 41.989 58.869
]
So please check _MMPBSA_complex.mdcrd.0, it expects 3(side lengths) values
for PBC Box cell dimensions or 6(3 side lengths and 3 angles alpha, beta,
gamma).
Alternatively strip out solvent and counter-ions from complex_solv.prmtop
using ante-MMPBSA.py, and also from trajectory and write trajectory without
box info with following commands in cpptraj
parm complex_solv.prmtop
trajin complex_solv.nc
strip :WAT,WAT,Na+,Cl- outprefix dry nobox
trajout complex_dry.nc nobox
and then try
On Thu, Jun 16, 2016 at 8:38 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’ve run successfully mmgbsa.py decomposition analysis, etc.
>
> I’ve used the same topology files and trajectory to run normal mode
> entropy calculation.
>
> My entropy.in file is:
>
> Input file for running entropy calculations using NMode
> &general
> endframe=10000, keep_files=2,
> /
> &nmode
> nmstartframe=6250, nmendframe=9750,
> nminterval=250, nmode_igb=1, nmode_istrng=0.1,
> /
>
> I got the following error message. Any help would be greatly appreciated
>
> Entropy gtzotzos$ mpirun -np 12 MMPBSA.py.MPI -O -i entropy.in -o
> FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP__MMPBSA.dat -sp
> complex_solv.prmtop -cp complex.prmtop -rp subA.prmtop -lp subB.prmtop -y
> *.nc
>
>
> Loading and checking parameter files for compatibility...
> cpptraj found! Using /Users/gtzotzos/Programs/MD/amber14/bin/cpptraj
> mmpbsa_py_nabnmode found! Using
> /Users/gtzotzos/Programs/MD/amber14/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation…
>
> Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 2
> Error: Box line=[ 41.989 58.869
> ]
>
> Error: Could not set up _MMPBSA_complex.mdcrd.0 for reading.
> Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
> File "/Users/gtzotzos/Programs/MD/amber14/bin/MMPBSA.py.MPI", line 103,
> in <module>
> app.file_setup()
> File
> "/Users/gtzotzos/Programs/MD/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 156, in file_setup
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> File
> "/Users/gtzotzos/Programs/MD/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 216, in make_trajectories
> (trj_suffix, i) for i in range(size)], cpptraj)
> File
> "/Users/gtzotzos/Programs/MD/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 467, in __init__
> self.Query()
> File
> "/Users/gtzotzos/Programs/MD/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 602, in Query
> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> TrajError: /Users/gtzotzos/Programs/MD/amber14/bin/cpptraj failed when
> querying _MMPBSA_complex.mdcrd.0
> Error occured on rank 0.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> Regards
>
> George
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 16 2016 - 10:30:02 PDT
