Hi,
I have been running single frame nmode analysis jobs on a series of complexes and have encountered an issue with my largest complex. The receptor is 562 residues/4373 atoms in size. The error I get upon job failure is:
FATAL: allocation failure in vector()
File "/usr/local/amber14/bin/MMPBSA.py", line 104, in <module>
app.run_mmpbsa()
File "/usr/local/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 321, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/usr/local/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
CalcError: /usr/local/amber14/bin/mmpbsa_py_nabnmode failed with prmtop ../1ER_4IH7_dry.prmtop!
Exiting. All files have been retained.
It appears it is failing due to insufficient memory. I previously ran this job on a supercomputer cluster and it was killed due to excessive memory usage. It had been allocated 4gb of memory for that job. I then re-ran it on my local workstation with at least 8 gb of memory available for the calculation (and got the error above). What steps do I need to take to reduce the memory requirement to get the calculation to finish successfully?
Thanks,
Nick
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Received on Mon Mar 21 2016 - 08:30:05 PDT
