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
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Received on Thu Jun 16 2016 - 08:30:03 PDT
