Hi......
I did the MD simulation with IGB= 7 and 8 solvent models and then tried to do the MMGBSA analysis but it crashes with the following error message:
/users2/local/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
File "/users/work/czarek/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/users2/local/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/users2/local/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/users2/local/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /users2/local/amber/amber16/bin/sander failed with prmtop complex.top!
Error occured on rank 3.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
For the complexes (Pdb :1BFC and 2JCQ) when I did the MD simulation with IGB=2 ,everything was fine with MMGBSA calculation using IGB=2.
For the same complexes (Pdb :1BFC and 2JCQ) simulated with IGB= 7 & 8, I tried to do the MMGBSA for the MD trajectories (IGB= 7 and 8) using both IGB = 2 and 7 or 8 and it crashes every time.
Could you please help me to solve the error...?
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Received on Fri Oct 06 2023 - 02:00:02 PDT
