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 Wed Dec 04 2019 - 21:00:01 PST
