/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
Error: Could not determine trajectory _MMPBSA_complex.mdcrd.0 format.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 95, in <module>
    app.file_setup()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 216, in make_trajectories
    (trj_suffix, i) for i in range(size)], cpptraj)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 467, in __init__
    self.Query()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /ncats/apps/hpc/amber14/bin/cpptraj failed when querying _MMPBSA_complex.mdcrd.0
Exiting. All files have been retained.
Error: Could not determine trajectory _MMPBSA_complex.mdcrd.0 format.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 95, in <module>
    app.file_setup()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 216, in make_trajectories
    (trj_suffix, i) for i in range(size)], cpptraj)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 467, in __init__
    self.Query()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /ncats/apps/hpc/amber14/bin/cpptraj failed when querying _MMPBSA_complex.mdcrd.0
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
Error: in read of Coords frame 1 of trajectory _MMPBSA_complex.mdcrd.0.
Error: Could not set up _MMPBSA_complex.mdcrd.0 for reading.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
	1 errors encountered reading input.
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 95, in <module>
    app.file_setup()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 238, in make_trajectories
    nmtraj.Run(pre + 'com_nm_traj_cpptraj.out')
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 684, in Run
    raise TrajError('Error running %s' % self.program)
AttributeError: 'Trajectory' object has no attribute 'program'
Exiting. All files have been retained.
Error: in read of Coords frame 1 of trajectory _MMPBSA_complex.mdcrd.0.
Error: Could not set up _MMPBSA_complex.mdcrd.0 for reading.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 95, in <module>
    app.file_setup()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 216, in make_trajectories
    (trj_suffix, i) for i in range(size)], cpptraj)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 467, in __init__
    self.Query()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /ncats/apps/hpc/amber14/bin/cpptraj failed when querying _MMPBSA_complex.mdcrd.0
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
Error: # atoms in TRX file (0) does not match # atoms in parm lig_vac.prmtop (42)
Error: Could not set up _MMPBSA_ligand.mdcrd.0 for reading.
Error: Could not set up input trajectory '_MMPBSA_ligand.mdcrd.0'.
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 95, in <module>
    app.file_setup()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
    self.mpi_size, str(external_progs['cpptraj']), self.pre)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 265, in make_trajectories
    (trj_suffix, i) for i in range(size)], cpptraj)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 467, in __init__
    self.Query()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py", line 602, in Query
    raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /ncats/apps/hpc/amber14/bin/cpptraj failed when querying _MMPBSA_ligand.mdcrd.0
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
  warn('Solvated topology %s has IFBOX == 0' % ifbox)
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
/ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
  File "/ncats/apps/hpc/amber14/bin/MMPBSA.py", line 96, in <module>
    app.run_mmpbsa()
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
    Calculation.run(self, rank, stdout=self.output % rank)
  File "/ncats/apps/hpc/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
    self.prmtop))
CalcError: /ncats/apps/hpc/amber14/bin/mmpbsa_py_nabnmode failed with prmtop com_vac.prmtop!
Exiting. All files have been retained.
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
