Does your *.nc file have box size? That's the error it is throwing up.
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]
That line suggests that it is looking for box coordinates (X, Y, Z
dimension + X, Y, Z angle) and it is not finding them.
Pietro
On 17/2/20 6:57 pm, Sruthi Sudhakar wrote:
> 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 - 03:00:01 PST
