[AMBER] MMPBSA failed

From: Albert <mailmd2011.gmail.com>
Date: Tue, 31 Jan 2017 08:28:55 +0100

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
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