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
/home/akinyemi/Amber20/amber20/bin/mmpbsa_py_energy
mmpbsa_py_nabnmode found! Using
/home/akinyemi/Amber20/amber20/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=[ 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>
app.file_setup()
File
"/home/akinyemi/Amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py",
line 155, in file_setup
self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
File
"/home/akinyemi/Amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py",
line 215, in make_trajectories
nmtraj = Trajectory(FILES.complex_prmtop, [pre + 'complex.%s.%d' %
File
"/home/akinyemi/Amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py",
line 467, in __init__
self.Query()
File
"/home/akinyemi/Amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py",
line 602, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /home/akinyemi/Amber20/amber20/bin/cpptraj failed when querying
_MMPBSA_complex.mdcrd.0
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed
calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
Best,
AKinyemi
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Received on Sat Nov 20 2021 - 17:00:02 PST
