Hello, I have got following error during MMPBSA.py calculation for PBSA MD
simulation.
How to fix it?
********************************************************************
Beginning GB calculations with
/home/mijiddorj/installs/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
mmpbsa_py_energy: malloc.c:2372: sysmalloc: Assertion `(old_top ==
(((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof
(struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long)
(old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
fd_nextsize))+((2 *(sizeof(size_t))) - 1)) & ~((2 *(sizeof(size_t))) - 1)))
&& ((old_top)->size & 0x1) && ((unsigned long) old_end & pagemask) == 0)'
failed.
File "/home/mijiddorj/installs/amber14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/main.py", line 218,
in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/calculation.py",
line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/mijiddorj/installs/amber14/bin/MMPBSA_mods/calculation.py",
line 148, in run
self.prmtop))
CalcError: /home/mijiddorj/installs/amber14/bin/mmpbsa_py_energy failed
with prmtop ../achol.prmtop!
Exiting. All files have been retained.
******************************************************
Best regaeds,
Mijiddorj
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Received on Tue Dec 01 2015 - 09:00:03 PST
