Hello, I am trying to perform MM/PBSA with following command:
mpirun -np 12 MMPBSA.py.MPI -O -i ../../infile/06-mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
-lp lig.prmtop -y prod*.mdcrd
But it constantly failed with the following messages:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /soft/amber/16/bin/mmpbsa_py_energy
cpptraj found! Using /soft/amber/16/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /soft/amber/16/bin/mmpbsa_py_energy
calculating complex contribution...
File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 476, in run
self.prmtop))
CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
Error occured on rank 8.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8
File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 476, in run
self.prmtop))
CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
Error occured on rank 9.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
I am just wondering where is the problem?
Thank you very much.
Albert
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Received on Mon Jan 30 2017 - 23:30:02 PST
