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mmpbsa with quasi-harmonic entropy approximation error
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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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