[AMBER] MMPBSA.py error

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Mon, 17 Feb 2020 16:27:54 +0530

Dear group members,
 I have been trying to do MMPBSA calculation on my complex but gettig the
following error:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
complex1_sol.prmtop -cp complex1.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y *.nc
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /apps/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /apps/amber18/bin/cpptraj
mmpbsa_py_nabnmode found! Using /apps/amber18/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 5
Error: Box line=[ 29.566 23.146 5.012 28.083 23.401
]
Error: Could not set up '_MMPBSA_complex.mdcrd.0' for reading.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
Error: Error(s) occurred during execution.
  File "/apps/amber18/bin/MMPBSA.py", line 99, in <module>
    app.file_setup()
  File "/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File
"/apps/amber18/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
"/apps/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line
467, in __init__
    self.Query()
  File
"/apps/amber18/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: /apps/amber18/bin/cpptraj failed when querying
_MMPBSA_complex.mdcrd.0
Exiting. All files have been retained.

 Please help me out to solve the error.

Sruthi


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Received on Mon Feb 17 2020 - 02:30:02 PST
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