This problem was solved by explicitly defining the strip_mask, receptor_mask and ligand_mask. Thank you!
Qing
At 2019-12-05 12:32:05, "Qing Lv" <lvqingjiejie.163.com> wrote:
>Hi All,
>
>
>I am trying to do MM/PBSA on several trajectories. Each time I got such errors:
>-------------------------------------------------------
>
>Running calculations on normal system...
>
>Beginning GB calculations with /xxxx/amber18/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/xxxx/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 478, in run
> self.prmtop))
>CalcError: /xxxx/amber18/bin/cpptraj failed with prmtop ../protein-lig.prmtop! ## PRMTOP of protein-ligand complex, with no solvent
>Error occured on rank 9.
>Exiting. All files have been retained.
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
>
>----------------------------
>
>
>This is my input file:
>Input file for running PB and GB
>&general
> startframe=51,interval=1, endframe=450, verbose=1,
> # entropy=1,
>/
>&gb
> igb=2, saltcon=0.100
>/
>&pb
> istrng=0.100,
>/
>
>
>
>But if I commented out the GB section, I got such errors: (error on ligand PRMTOP file)
>--------------------------------------------------------------------------
>Running calculations on normal system...
>
>Beginning PB calculations with /xxxx/amber18/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> File "/xxxx/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/xxxx/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
>CalcError: /xxxx/amber18/bin/mmpbsa_py_energy failed with prmtop ../lig.prmtop! ## PRMTOP of the ligand
>
>Error occured on rank 11.
>Exiting. All files have been retained.
>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11
>---------------------------------------------
>It seemed that PB calculation met no problem with the PRMTOP of protein-ligand complex, but had problems with the ligand PRMTOP file.
>
>
>The protein-lig.prmtop and lig.prmtop were generated during the MD setting up and should not have errors. I tried all the three trajectories and got the same errors. And I cannot get further error information.
>
>
>Could anyone help?
>
>
>
>Thanks a lot,
>Qing
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Received on Thu Dec 05 2019 - 00:00:02 PST
