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@davipatti
Created June 20, 2015 13:57
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mmpbsa with quasi-harmonic entropy approximation error
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /Users/david/bin/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /Users/david/bin/amber14/bin/cpptraj
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /Users/david/bin/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning quasi-harmonic calculations with /Users/david/bin/amber14/bin/cpptraj
Error: DataSet_Modes: bad eigenvalue 0 = 0.000000
Error: in Analysis # 0
Error: DataSet_Modes: bad eigenvalue 0 = 0.000000
Error: in Analysis # 1
Error: DataSet_Modes: bad eigenvalue 0 = 0.000000
Error: in Analysis # 2
File "/Users/david/bin/amber14/bin/MMPBSA.py", line 104, in <module>
app.run_mmpbsa()
File "/Users/david/bin/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/Users/david/bin/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/Users/david/bin/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 375, in run
Calculation.run(self, rank, stdout=self.output)
File "/Users/david/bin/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /Users/david/bin/amber14/bin/cpptraj failed with prmtop com.top!
Exiting. All files have been retained.
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