Hello:
I am trying to perform QM/GBSA with mmpbsa.py script. Here is my input file:
&general
endframe=400, interval=20,keep_files=0,
/
&gb
igb=5, saltcon=0.1, qmcharge_com=0, ifqnt=1,
qmcharge_lig=0,
qm_residues='1,377,345,249,278,245,347,242,321,337,248,293,285,283,282'
qm_theory='PM3',
/
I run the job with command line:
mpirun -np 16 MMPBSA.py.MPI -O -i qmpbsa.in -o QM_MMPBSA.dat -cp
com.prmtop -rp rec.prmtop -lp lig.prmtop -y pbsa.dcd >log
However, the job failed with messages:
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander 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
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 11.
Exiting. All files have been retained.
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 7.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 4.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander 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
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 14.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14
File "/home/albert/install/amber14/bin/MMPBSA.py.MPI", line 104, in
<module>
app.run_mmpbsa()
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/albert/install/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/albert/install/amber14/bin/sander failed with prmtop
com.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
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Received on Wed Jul 22 2015 - 00:30:02 PDT
