sander failed with prmtop COM.prmtop!

[Sanjay Kumar]

I performed the decomposition analysis 

one of my systems failed and showed this error, can you figure out where I miss it.

CHAMBER prmtops found. Forcing use of sander
Preparing trajectories for simulation...
96 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/ravishankar/.conda/envs/AmberTools21/bin/sander
  calculating complex contribution...
 bad atom type: i
  File "/usr/local/bin/gmx_MMPBSA", line 11, in <module>
    sys.exit(gmxmmpbsa())
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/app.py", line 113, in gmxmmpbsa
    app.run_mmpbsa()
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/main.py", line 212, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/calculation.py", line 84, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/usr/local/lib/python3.6/site-packages/GMXMMPBSA/calculation.py", line 159, in run
    self.prmtop))
CalcError: /home/ravishankar/.conda/envs/AmberTools21/bin/sander failed with prmtop COM.prmtop!
Exiting. All files have been retained.

[Mario Sergio Valdes]

Please check this issue (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/95) and make sure you don't have a similar problem. Usually, this is because your trajectory or the structure you used have PBC so they are not consistent.

Mario S.