[AMBER] Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 5

From: Akinyemi Omoniyi <aaomoniyi2014.gmail.com>
Date: Sun, 21 Nov 2021 01:47:45 +0100

Dear All,

I encountered this error when running a normal mode analysis of a
protein-protein system.
Please, how can I solve this problem?

AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
complex_solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y prod_autoimage.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/akinyemi/Amber20/amber20/bin/cpptraj
mmpbsa_py_energy found! Using
mmpbsa_py_nabnmode found! Using
Preparing trajectories for simulation...
Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 5
Error: Box line=[ 84.508 30.177 135.821 89.524 107.890
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 "/home/akinyemi/Amber20/amber20/bin/MMPBSA.py", line 99, in <module>
line 155, in file_setup
    self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
line 215, in make_trajectories
    nmtraj = Trajectory(FILES.complex_prmtop, [pre + 'complex.%s.%d' %
line 467, in __init__
line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /home/akinyemi/Amber20/amber20/bin/cpptraj failed when querying

Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.

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Received on Sat Nov 20 2021 - 17:00:02 PST
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