The error says "Solvated topology 0 has IFBOX == 0"
This is odd because you said you did the md in GB. Is there perhaps water
in your system? Check and see.
On Fri, Oct 6, 2023, 4:33 AM Anila Sebastian via AMBER <amber.ambermd.org>
wrote:
> 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 - 03:30:02 PDT
